Sample records for cancer methods analysis

  1. Comparison of linear discriminant analysis methods for the classification of cancer based on gene expression data

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    He Miao


    Full Text Available Abstract Background More studies based on gene expression data have been reported in great detail, however, one major challenge for the methodologists is the choice of classification methods. The main purpose of this research was to compare the performance of linear discriminant analysis (LDA and its modification methods for the classification of cancer based on gene expression data. Methods The classification performance of linear discriminant analysis (LDA and its modification methods was evaluated by applying these methods to six public cancer gene expression datasets. These methods included linear discriminant analysis (LDA, prediction analysis for microarrays (PAM, shrinkage centroid regularized discriminant analysis (SCRDA, shrinkage linear discriminant analysis (SLDA and shrinkage diagonal discriminant analysis (SDDA. The procedures were performed by software R 2.80. Results PAM picked out fewer feature genes than other methods from most datasets except from Brain dataset. For the two methods of shrinkage discriminant analysis, SLDA selected more genes than SDDA from most datasets except from 2-class lung cancer dataset. When comparing SLDA with SCRDA, SLDA selected more genes than SCRDA from 2-class lung cancer, SRBCT and Brain dataset, the result was opposite for the rest datasets. The average test error of LDA modification methods was lower than LDA method. Conclusions The classification performance of LDA modification methods was superior to that of traditional LDA with respect to the average error and there was no significant difference between theses modification methods.

  2. Optimized Method for Untargeted Metabolomics Analysis of MDA-MB-231 Breast Cancer Cells

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    Amanda L. Peterson


    Full Text Available Cancer cells often have dysregulated metabolism, which is largely characterized by the Warburg effect—an increase in glycolytic activity at the expense of oxidative phosphorylation—and increased glutamine utilization. Modern metabolomics tools offer an efficient means to investigate metabolism in cancer cells. Currently, a number of protocols have been described for harvesting adherent cells for metabolomics analysis, but the techniques vary greatly and they lack specificity to particular cancer cell lines with diverse metabolic and structural features. Here we present an optimized method for untargeted metabolomics characterization of MDA-MB-231 triple negative breast cancer cells, which are commonly used to study metastatic breast cancer. We found that an approach that extracted all metabolites in a single step within the culture dish optimally detected both polar and non-polar metabolite classes with higher relative abundance than methods that involved removal of cells from the dish. We show that this method is highly suited to diverse applications, including the characterization of central metabolic flux by stable isotope labelling and differential analysis of cells subjected to specific pharmacological interventions.

  3. A Mass Spectrometric Analysis Method Based on PPCA and SVM for Early Detection of Ovarian Cancer. (United States)

    Wu, Jiang; Ji, Yanju; Zhao, Ling; Ji, Mengying; Ye, Zhuang; Li, Suyi


    Background. Surfaced-enhanced laser desorption-ionization-time of flight mass spectrometry (SELDI-TOF-MS) technology plays an important role in the early diagnosis of ovarian cancer. However, the raw MS data is highly dimensional and redundant. Therefore, it is necessary to study rapid and accurate detection methods from the massive MS data. Methods. The clinical data set used in the experiments for early cancer detection consisted of 216 SELDI-TOF-MS samples. An MS analysis method based on probabilistic principal components analysis (PPCA) and support vector machine (SVM) was proposed and applied to the ovarian cancer early classification in the data set. Additionally, by the same data set, we also established a traditional PCA-SVM model. Finally we compared the two models in detection accuracy, specificity, and sensitivity. Results. Using independent training and testing experiments 10 times to evaluate the ovarian cancer detection models, the average prediction accuracy, sensitivity, and specificity of the PCA-SVM model were 83.34%, 82.70%, and 83.88%, respectively. In contrast, those of the PPCA-SVM model were 90.80%, 92.98%, and 88.97%, respectively. Conclusions. The PPCA-SVM model had better detection performance. And the model combined with the SELDI-TOF-MS technology had a prospect in early clinical detection and diagnosis of ovarian cancer.

  4. A Mass Spectrometric Analysis Method Based on PPCA and SVM for Early Detection of Ovarian Cancer

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    Jiang Wu


    Full Text Available Background. Surfaced-enhanced laser desorption-ionization-time of flight mass spectrometry (SELDI-TOF-MS technology plays an important role in the early diagnosis of ovarian cancer. However, the raw MS data is highly dimensional and redundant. Therefore, it is necessary to study rapid and accurate detection methods from the massive MS data. Methods. The clinical data set used in the experiments for early cancer detection consisted of 216 SELDI-TOF-MS samples. An MS analysis method based on probabilistic principal components analysis (PPCA and support vector machine (SVM was proposed and applied to the ovarian cancer early classification in the data set. Additionally, by the same data set, we also established a traditional PCA-SVM model. Finally we compared the two models in detection accuracy, specificity, and sensitivity. Results. Using independent training and testing experiments 10 times to evaluate the ovarian cancer detection models, the average prediction accuracy, sensitivity, and specificity of the PCA-SVM model were 83.34%, 82.70%, and 83.88%, respectively. In contrast, those of the PPCA-SVM model were 90.80%, 92.98%, and 88.97%, respectively. Conclusions. The PPCA-SVM model had better detection performance. And the model combined with the SELDI-TOF-MS technology had a prospect in early clinical detection and diagnosis of ovarian cancer.

  5. Comparative analysis of methods for identifying recurrent copy number alterations in cancer.

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    Xiguo Yuan

    Full Text Available Recurrent copy number alterations (CNAs play an important role in cancer genesis. While a number of computational methods have been proposed for identifying such CNAs, their relative merits remain largely unknown in practice since very few efforts have been focused on comparative analysis of the methods. To facilitate studies of recurrent CNA identification in cancer genome, it is imperative to conduct a comprehensive comparison of performance and limitations among existing methods. In this paper, six representative methods proposed in the latest six years are compared. These include one-stage and two-stage approaches, working with raw intensity ratio data and discretized data respectively. They are based on various techniques such as kernel regression, correlation matrix diagonal segmentation, semi-parametric permutation and cyclic permutation schemes. We explore multiple criteria including type I error rate, detection power, Receiver Operating Characteristics (ROC curve and the area under curve (AUC, and computational complexity, to evaluate performance of the methods under multiple simulation scenarios. We also characterize their abilities on applications to two real datasets obtained from cancers with lung adenocarcinoma and glioblastoma. This comparison study reveals general characteristics of the existing methods for identifying recurrent CNAs, and further provides new insights into their strengths and weaknesses. It is believed helpful to accelerate the development of novel and improved methods.

  6. Comparative Analysis of Feature Extraction Methods for the Classification of Prostate Cancer from TRUS Medical Images

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    Manavalan Radhakrishnan


    Full Text Available Diagnosing Prostate cancer is a challenging task for Urologists, Radiologists, and Oncologists. Ultrasound imaging is one of the hopeful techniques used for early detection of prostate cancer. The Region of interest (ROI is identified by different methods after preprocessing. In this paper, DBSCAN clustering with morphological operators is used to extort the prostate region. The evaluation of texture features is important for several image processing applications. The performance of the features extracted from the various texture methods such as histogram, Gray Level Cooccurrence Matrix (GLCM, Gray-Level Run-Length Matrix (GRLM, are analyzed separately. In this paper, it is proposed to combine histogram, GLRLM and GLCM in order to study the performance. The Support Vector Machine (SVM is adopted to classify the extracted features into benign or malignant. The performance of texture methods are evaluated using various statistical parameters such as sensitivity, specificity and accuracy. The comparative analysis has been performed over 5500 digitized TRUS images of prostate.

  7. Quantitative Analysis of Differential Proteome Expression in Bladder Cancer vs. Normal Bladder Cells Using SILAC Method.

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    Ganglong Yang

    Full Text Available The best way to increase patient survival rate is to identify patients who are likely to progress to muscle-invasive or metastatic disease upfront and treat them more aggressively. The human cell lines HCV29 (normal bladder epithelia, KK47 (low grade nonmuscle invasive bladder cancer, NMIBC, and YTS1 (metastatic bladder cancer have been widely used in studies of molecular mechanisms and cell signaling during bladder cancer (BC progression. However, little attention has been paid to global quantitative proteome analysis of these three cell lines. We labeled HCV29, KK47, and YTS1 cells by the SILAC method using three stable isotopes each of arginine and lysine. Labeled proteins were analyzed by 2D ultrahigh-resolution liquid chromatography LTQ Orbitrap mass spectrometry. Among 3721 unique identified and annotated proteins in KK47 and YTS1 cells, 36 were significantly upregulated and 74 were significantly downregulated with >95% confidence. Differential expression of these proteins was confirmed by western blotting, quantitative RT-PCR, and cell staining with specific antibodies. Gene ontology (GO term and pathway analysis indicated that the differentially regulated proteins were involved in DNA replication and molecular transport, cell growth and proliferation, cellular movement, immune cell trafficking, and cell death and survival. These proteins and the advanced proteome techniques described here will be useful for further elucidation of molecular mechanisms in BC and other types of cancer.

  8. Studies on retrospective analysis of leading primary cancers and improvement of cancer treatment method in Korea cancer center hospital

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    Lee, Jong In; Lee, Kang Hyun; Choi, Soo Yong; Kim, Ki Wha; Kang, Sung Mok


    a. Retrospective studies included cancers of the stomach, breast, bladder, salivary gland, thyroid, esophagus, endometrium and ovary. (1) Study cancers were analyzed about clinical characteristics, prognostic factors influenced on survival time, survival rate, etc. (2) Among 5,305 study patients, 1,405(26.5%) were identified with death, 3,485(65.7%) were alive and 415(7.8%) were not identified. b. Prospective studies included 10 subjects such as bladder cancer, retinoblastoma, malignant patients, gastric cancer, uterine cervix cancer and ovary cancer. We are continuing registering eligible study patients. c. Results for 11 papers were published at the journal. d. We established follow-up system in order to identify the survival for study subjects through National Statistical Office, Government Provincial Office and Cancer Registration System at Korea Cancer Center Hospital. e. At present, we are establishing computerized registration system about case report form for study cancers.

  9. Cancer panomics: computational methods and infrastructure for integrative analysis of cancer high-throughput "omics" data

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    Brunak, Søren; De La Vega, Francisco M.; Rätsch, Gunnar


    Targeted cancer treatment is becoming the goal of newly developed oncology medicines and has already shown promise in some spectacular cases such as the case of BRAF kinase inhibitors in BRAF-mutant (e.g. V600E) melanoma. These developments are driven by the advent of high-throughput sequencing...

  10. Quantitative analysis of collagen change between normal and cancerous thyroid tissues based on SHG method (United States)

    Chen, Xiwen; Huang, Zufang; Xi, Gangqin; Chen, Yongjian; Lin, Duo; Wang, Jing; Li, Zuanfang; Sun, Liqing; Chen, Jianxin; Chen, Rong


    Second-harmonic generation (SHG) is proved to be a high spatial resolution, large penetration depth and non-photobleaching method. In our study, SHG method was used to investigate the normal and cancerous thyroid tissue. For SHG imaging performance, system parameters were adjusted for high-contrast images acquisition. Each x-y image was recorded in pseudo-color, which matches the wavelength range in the visible spectrum. The acquisition time for a 512×512-pixels image was 1.57 sec; each acquired image was averaged four frames to improve the signal-to-noise ratio. Our results indicated that collagen presence as determined by counting the ratio of the SHG pixels over the whole pixels for normal and cancerous thyroid tissues were 0.48+/-0.05, 0.33+/-0.06 respectively. In addition, to quantitatively assess collagen-related changes, we employed GLCM texture analysis to the SHG images. Corresponding results showed that the correlation both fell off with distance in normal and cancerous group. Calculated value of Corr50 (the distance where the correlation crossed 50% of the initial correlation) indicated significant difference. This study demonstrates that SHG method can be used as a complementary tool in thyroid histopathology.

  11. Analysis of secretome of breast cancer cell line with an optimized semi-shotgun method

    Institute of Scientific and Technical Information of China (English)

    TANG Xiaorong; YAO Ling; CHEN Keying; HU Xiaofang; XU Lisa X.; FAN Chunhai


    Secretome,the totality of secreted proteins,is viewed as a promising pool of candidate cancer biomarkers.Simple and reliable methods for identifying secreted proteins are highly desired.We used an optimized semi-shotgun liquid chromatography followed by tandem mass spectrometry (LC-MS/MS) method to analyze the secretome of breast cancer cell line MDA-MB-231.A total of 464 proteins were identified.About 63% of the proteins were classified as secreted proteins,including many promising breast cancer biomarkers,which were thought to be correlated with tumorigenesis,tumor development and metastasis.These results suggest that the optimized method may be a powerful strategy for cell line secretome profiling,and can be used to find potential cancer biomarkers with great clinical significance.

  12. Comparing paraffined and deparaffinized breast cancer tissue samples and an analysis of Raman spectroscopy and infrared methods (United States)

    Depciuch, J.; Kaznowska, E.; Szmuc, K.; Zawlik, I.; Cholewa, M.; Heraud, P.; Cebulski, J.


    Breast cancer makes up a quarter of all cancer in women, which is why research into new diagnostic methods and sample preparations need to be developed at an accelerated pace. Researchers are looking for diagnostic tools to detect when an individual has cancer cells and use that information to see what measurements and approaches can be used to take further diagnostic steps. The most common method of sample preparation is the imbibing of tumor tissue in paraffin, which can produce a background for spectroscopic measurements in the range of 500-3500 cm-1. In this study we demonstrated that proper preparation of paraffin-embedded specimens and the measurement methodology can eliminate paraffin vibration, as was done in the work Depciuch et al. 2015. Thanks to this spectroscopic technique there may become a reliable and accurate method of diagnosing breast cancer based on the evidence found from the prepared samples. The study compared the results obtained through Raman spectroscopy and FTIR (Fourier Transform Infrared) measurements of healthy and cancerous breast tissues that were either embedded in paraffin or deparaffinized. The resulting spectrum and accurate analysis led to the conclusion that the appropriate measurement of the background and the elimination of peaks from the paraffin had the greatest impact on the reliability of results. Furthermore, after the accurate, detailed studies FTIR and Raman spectroscopy on samples of breast tissue that were deparaffinized or embedded in paraffin, including a complete analysis of the peak after transformation Kramers-Kröning (KK), it was found that sample preparation did not affect the result obtained by measuring the reflectance in the mid-infrared range, and that this only had a minimal effect relating to the intensity obtained by the measurement of the Raman peak. Only in special cases, when Raman spectroscopic methods are used for research to find the peculiarities of the spectra, are deparaffinization recommended

  13. Comparing 3 dietary pattern methods--cluster analysis, factor analysis, and index analysis--With colorectal cancer risk: The NIH-AARP Diet and Health Study. (United States)

    Reedy, Jill; Wirfält, Elisabet; Flood, Andrew; Mitrou, Panagiota N; Krebs-Smith, Susan M; Kipnis, Victor; Midthune, Douglas; Leitzmann, Michael; Hollenbeck, Albert; Schatzkin, Arthur; Subar, Amy F


    The authors compared dietary pattern methods-cluster analysis, factor analysis, and index analysis-with colorectal cancer risk in the National Institutes of Health (NIH)-AARP Diet and Health Study (n = 492,306). Data from a 124-item food frequency questionnaire (1995-1996) were used to identify 4 clusters for men (3 clusters for women), 3 factors, and 4 indexes. Comparisons were made with adjusted relative risks and 95% confidence intervals, distributions of individuals in clusters by quintile of factor and index scores, and health behavior characteristics. During 5 years of follow-up through 2000, 3,110 colorectal cancer cases were ascertained. In men, the vegetables and fruits cluster, the fruits and vegetables factor, the fat-reduced/diet foods factor, and all indexes were associated with reduced risk; the meat and potatoes factor was associated with increased risk. In women, reduced risk was found with the Healthy Eating Index-2005 and increased risk with the meat and potatoes factor. For men, beneficial health characteristics were seen with all fruit/vegetable patterns, diet foods patterns, and indexes, while poorer health characteristics were found with meat patterns. For women, findings were similar except that poorer health characteristics were seen with diet foods patterns. Similarities were found across methods, suggesting basic qualities of healthy diets. Nonetheless, findings vary because each method answers a different question.

  14. Prostate cancer and quality of life: analysis of response shift using triangulation between methods. (United States)

    Serdà I Ferrer, Bernat-Carles; Valle, Arantza Del; Marcos-Gragera, Rafael


    Quality of life (QoL) after prostate cancer treatment is uncertain. Patient responses to QoL questions shift for a number of reasons: measurement intervals no longer have the same psychological anchors (recalibration), the importance attributed to different QoL domains changes over time (reprioritization), and the definition of QoL differs throughout the disease continuum (reconceptualization). Therefore, the aim of this study was to describe QoL response shift in a cohort of 66 men with prostate cancer. The method involved carrying out a sequential triangulation between quantitative and qualitative methods. Patients were assessed at baseline (P1), followed by a posttest (P2) and a then-test measurement (P3). The difference between P3 and P1 was used to determine the response shift effect (recalibration). From baseline to posttest, QoL significantly decreased. The recalibration then-test confirmed a low QoL in all periods evaluated. Coping mechanisms were found to differ by age group, with older men less concerned about side effects than younger men. Health professionals should be alert to QoL changes over time and possible side effects, should coping skills fail.

  15. Automated Method for Analysis of Mammographic Breast Density - A Technique for Breast Cancer Risk Estimation (United States)


    mammographic density: Implications for under- standing breast cancer,’’ J. Natl. Cancer Inst. 89, 531–532 ~1997!. 10 W. Leung, F. Goldberg, B. Zee ... Mexico . Radiology 1998;209:511–518. 4. Boyd NF, Byng RA, Jong EK, et al. Quantita- tive classification of mammographic densi- ties and breast cancer risk

  16. Methods for predicting anti-cancer response

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    The present invention relates to methods for predicting response of a cancer in a subject to anti-cancer therapies based upon a determination and analysis of a chromosomal aberration score, such as the number of allelic imbalance or the number of telomeric allelic imbalance in the chromosomes...

  17. Saliva collection methods for DNA biomarker analysis in oral cancer patients. (United States)

    Matthews, April M; Kaur, Harpal; Dodd, Michael; D'Souza, Jacob; Liloglou, Triantafillos; Shaw, Richard J; Risk, Janet M


    Patients with head and neck cancers are predisposed to local recurrence and second primaries because of the phenomenon of field cancerisation, and clinical detection of recurrence remains challenging. DNA biomarkers in saliva may prove to be an adjunct to current diagnostic methods, but irradiation of the primary site often leads to xerostomia. We assessed 3 methods of collecting saliva for their ability to generate DNA of sufficient quantity and quality to use in biomarker assays. Paired saliva samples were collected from 2 groups of patients with oral squamous cell carcinoma (SCC). In the first group saliva was collected in Oragene(®) vials and as saline mouthwash from non-irradiated patients (n=21) (4 had had radiotherapy before collection); in the second group it was collected using Oragene(®) sponge kits and as mouthwash from irradiated patients (n=24). Quantitative polymerase chain reaction (qPCR) showed that Oragene(®) vials contained DNA in significantly greater amounts (median 122 μg, range 4-379) than mouthwash (median 17 μg, range 2-194) (p=0.0001) in the non-irradiated patients, while Oragene(®) sponge kits (median 4 μg, range 0.1-61) and mouthwash (median 5.5 μg, range 0.1-75) generated comparable concentrations of DNA from the irradiated group. All 90 samples contained DNA of sufficient quantity and quality for p16 promoter quantitative methylation-specific PCR (qMSP). While Oragene(®) vials contained the most DNA, all 3 methods yielded enough to detect DNA biomarkers using qMSP. The method of collection should depend on the compliance of the patient and oral competency.

  18. A New Cell Block Method for Multiple Immunohistochemical Analysis of Circulating Tumor Cells in Patients with Liver Cancer (United States)

    Nam, Soo Jeong; Yeo, Hyun Yang; Chang, Hee Jin; Kim, Bo Hyun; Hong, Eun Kyung; Park, Joong-Won


    Purpose We developed a new method of detecting circulating tumor cells (CTCs) in liver cancer patients by constructing cell blocks from peripheral blood cells, including CTCs, followed by multiple immunohistochemical analysis. Materials and Methods Cell blockswere constructed from the nucleated cell pellets of peripheral blood afterremoval of red blood cells. The blood cell blocks were obtained from 29 patients with liver cancer, and from healthy donor blood spikedwith seven cell lines. The cell blocks and corresponding tumor tissues were immunostained with antibodies to seven markers: cytokeratin (CK), epithelial cell adhesion molecule (EpCAM), epithelial membrane antigen (EMA), CK18, α-fetoprotein (AFP), Glypican 3, and HepPar1. Results The average recovery rate of spiked SW620 cells from blood cell blocks was 91%. CTCs were detected in 14 out of 29 patients (48.3%); 11/23 hepatocellular carcinomas (HCC), 1/2 cholangiocarcinomas (CC), 1/1 combined HCC-CC, and 1/3 metastatic cancers. CTCs from 14 patients were positive for EpCAM (57.1%), EMA (42.9%), AFP (21.4%), CK18 (14.3%), Gypican3 and CK (7.1%, each), and HepPar1 (0%). Patients with HCC expressed EpCAM, EMA, CK18, and AFP in tissue and/or CTCs, whereas CK, HepPar1, and Glypican3 were expressed only in tissue. Only EMA was significantly associated with the expressions in CTC and tissue. CTC detection was associated with higher T stage and portal vein invasion in HCC patients. Conclusion This cell block method allows cytologic detection and multiple immunohistochemical analysis of CTCs. Our results show that tissue biomarkers of HCC may not be useful for the detection of CTC. EpCAM could be a candidate marker for CTCs in patients with HCC. PMID:27034142

  19. Integration Analysis of Three Omics Data Using Penalized Regression Methods: An Application to Bladder Cancer. (United States)

    Pineda, Silvia; Real, Francisco X; Kogevinas, Manolis; Carrato, Alfredo; Chanock, Stephen J; Malats, Núria; Van Steen, Kristel


    Omics data integration is becoming necessary to investigate the genomic mechanisms involved in complex diseases. During the integration process, many challenges arise such as data heterogeneity, the smaller number of individuals in comparison to the number of parameters, multicollinearity, and interpretation and validation of results due to their complexity and lack of knowledge about biological processes. To overcome some of these issues, innovative statistical approaches are being developed. In this work, we propose a permutation-based method to concomitantly assess significance and correct by multiple testing with the MaxT algorithm. This was applied with penalized regression methods (LASSO and ENET) when exploring relationships between common genetic variants, DNA methylation and gene expression measured in bladder tumor samples. The overall analysis flow consisted of three steps: (1) SNPs/CpGs were selected per each gene probe within 1Mb window upstream and downstream the gene; (2) LASSO and ENET were applied to assess the association between each expression probe and the selected SNPs/CpGs in three multivariable models (SNP, CPG, and Global models, the latter integrating SNPs and CPGs); and (3) the significance of each model was assessed using the permutation-based MaxT method. We identified 48 genes whose expression levels were significantly associated with both SNPs and CPGs. Importantly, 36 (75%) of them were replicated in an independent data set (TCGA) and the performance of the proposed method was checked with a simulation study. We further support our results with a biological interpretation based on an enrichment analysis. The approach we propose allows reducing computational time and is flexible and easy to implement when analyzing several types of omics data. Our results highlight the importance of integrating omics data by applying appropriate statistical strategies to discover new insights into the complex genetic mechanisms involved in disease

  20. Minimally Invasive Methods for Staging in Lung Cancer: Systematic Review and Meta-Analysis

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    Gonzalo Labarca


    Full Text Available Introduction. Endobronchial ultrasound (EBUS is a procedure that provides access to the mediastinal staging; however, EBUS cannot be used to stage all of the nodes in the mediastinum. In these cases, endoscopic ultrasound (EUS is used for complete staging. Objective. To provide a synthesis of the evidence on the diagnostic performance of EBUS + EUS in patients undergoing mediastinal staging. Methods. Systematic review and meta-analysis to evaluate the diagnostic yield of EBUS + EUS compared with surgical staging. Two researchers performed the literature search, quality assessments, data extractions, and analyses. We produced a meta-analysis including sensitivity, specificity, and likelihood ratio analysis. Results. Twelve primary studies (1515 patients were included; two were randomized controlled trials (RCTs and ten were prospective trials. The pooled sensitivity for combined EBUS + EUS was 87% (CI 84–89% and the specificity was 99% (CI 98–100%. For EBUS + EUS performed with a single bronchoscope group, the sensitivity improved to 88% (CI 83.1–91.4% and specificity improved to 100% (CI 99-100%. Conclusion. EBUS + EUS is a highly accurate and safe procedure. The combined procedure should be considered in selected patients with lymphadenopathy noted at stations that are not traditionally accessible with conventional EBUS.

  1. Assessment of FBA Based Gene Essentiality Analysis in Cancer with a Fast Context-Specific Network Reconstruction Method.

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    Luis Tobalina

    Full Text Available Gene Essentiality Analysis based on Flux Balance Analysis (FBA-based GEA is a promising tool for the identification of novel metabolic therapeutic targets in cancer. The reconstruction of cancer-specific metabolic networks, typically based on gene expression data, constitutes a sensible step in this approach. However, to our knowledge, no extensive assessment on the influence of the reconstruction process on the obtained results has been carried out to date.In this article, we aim to study context-specific networks and their FBA-based GEA results for the identification of cancer-specific metabolic essential genes. To that end, we used gene expression datasets from the Cancer Cell Line Encyclopedia (CCLE, evaluating the results obtained in 174 cancer cell lines. In order to more clearly observe the effect of cancer-specific expression data, we did the same analysis using randomly generated expression patterns. Our computational analysis showed some essential genes that are fairly common in the reconstructions derived from both gene expression and randomly generated data. However, though of limited size, we also found a subset of essential genes that are very rare in the randomly generated networks, while recurrent in the sample derived networks, and, thus, would presumably constitute relevant drug targets for further analysis. In addition, we compare the in-silico results to high-throughput gene silencing experiments from Project Achilles with conflicting results, which leads us to raise several questions, particularly the strong influence of the selected biomass reaction on the obtained results. Notwithstanding, using previous literature in cancer research, we evaluated the most relevant of our targets in three different cancer cell lines, two derived from Gliobastoma Multiforme and one from Non-Small Cell Lung Cancer, finding that some of the predictions are in the right track.

  2. Comparison of Predicted Probabilities of Proportional Hazards Regression and Linear Discriminant Analysis Methods Using a Colorectal Cancer Molecular Biomarker Database

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    Upender Manne


    Full Text Available Background: Although a majority of studies in cancer biomarker discovery claim to use proportional hazards regression (PHREG to the study the ability of a biomarker to predict survival, few studies use the predicted probabilities obtained from the model to test the quality of the model. In this paper, we compared the quality of predictions by a PHREG model to that of a linear discriminant analysis (LDA in both training and test set settings. Methods: The PHREG and LDA models were built on a 491 colorectal cancer (CRC patient dataset comprised of demographic and clinicopathologic variables, and phenotypic expression of p53 and Bcl-2. Two variable selection methods, stepwise discriminant analysis and the backward selection, were used to identify the final models. The endpoint of prediction in these models was five-year post-surgery survival. We also used linear regression model to examine the effect of bin size in the training set on the accuracy of prediction in the test set.Results: The two variable selection techniques resulted in different models when stage was included in the list of variables available for selection. However, the proportion of survivors and non-survivors correctly identified was identical in both of these models. When stage was excluded from the variable list, the error rate for the LDA model was 42% as compared to an error rate of 34% for the PHREG model.Conclusions: This study suggests that a PHREG model can perform as well or better than a traditional classifier such as LDA to classify patients into prognostic classes. Also, this study suggests that in the absence of the tumor stage as a variable, Bcl-2 expression is a strong prognostic molecular marker of CRC.

  3. Radioimmunoassay method suitable for analysis of salivary cortisol in patients with breast cancer in treatment by teletherapy - a preliminary study

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    Souza, Kellen Verena S. [Departamento de Engenharia Nuclear. Universidade Federal de Minas Gerais, Pampulha, MG (Brazil); Santos, Jane Lima dos [Departamento de Ciencias Biologicas, Universidade Estadual de Santa Cruz, Ilheus, BA (Brazil)


    Determination of salivary cortisol using radioimmunoassay and the relationship between stress levels were investigated before and after of the psychological intervention of 21 patients during teletherapy treatment of breast cancer. The benefits of psychological intervention during cancer treatment has been observed in some studies and evidence show that the patient's emotional state directly influences adherence to treatment, good prognosis and under stress. Thus, in present study 21 patients aged 50-70 years, females in the treatment of breast cancer at the Radiotherapy Service of Santa Casa de Misericordia in Belo Horizonte, were divided randomly into two groups: control (without psychological intervention) and Group TCC (with psychological intervention). Salivary cortisol concentrations are reportedly about 5.10% of those in serum, the levels has been used as an objective marker of hypothalamic-pituitary-adrenal (HPA) axis activity and avoided the confounding effects of venepuncture stress on cortisol levels. The assessment of cortisol in saliva has proven a valid and reliable measure of unbound steroid in the circulation. The salivary cortisol measured by radioimmunoassay in control patients and TCC showed no significant differences. The radioimmunoassay method show be suitable for analysis of salivary cortisol because allows measure low detection limits and have high sensibility. The values of TCC group and Control group were higher than reference values, except for one patient of the control group. At the beginning of treatment, both groups were homogeneous for Teletherapy. Both the TCC group as the control group had . 80% of participants in phase with stress. It was observed in the TCC group after radiotherapy showing a reversal 60% of participants without stress. The data show that cognitive-behavioral therapy has benefits for the control of psychological stress and enhance relevance of the psychologist to provide reduction or stress control during

  4. An IARC Manual series aimed at assisting cancer epidemiology and prevention. "Environmental carcinogens: selected methods of analysis". (United States)

    O'Neill, I K; Fishbein, L


    Since 1975, the IARC has been preparing a series of volumes entitled "Environmental Carcinogens: Selected Methods of Analysis" (IARC Manual series) of which the purposes are to assist analysts, epidemiologists and regulatory authorities in planning or performing exposure measurements that are truly comparable between different studies. The Manual series provides expert information within each volume on multi-media sampling, methods of analyses and some background of epidemiology, metabolism, use/occurrence for a group of known or suspect carcinogens. So far, eleven volumes have been published or are in preparation on the following subjects: N-nitrosamines, vinyl chloride, PAH, aromatic amines, mycotoxins, N-nitroso compounds, volatile halogenated hydrocarbons, metals, passive smoking, benzene and alkylated benzenes, dioxins, PCDFs and PCBs. The presentation will discuss needs and priorities for use of analytical chemistry in estimating exposures of apparently greatest relevance to cancer causation, i.e. the approach to developing this series. Indications from epidemiology, evaluations of carcinogenic risk to humans, and recent developments in total exposure assessment are that new methods and matrices need more emphasis, e.g. as with biochemical dosimetry, exhaled breath, and in indoor air.

  5. Critical analysis of imaging methods for the detection and diagnosis of breast cancer; Analise critica dos metodos de imagem na deteccao e diagnostico do cancer mamario

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    Mendonca, Maria Helena Siqueira


    Breast cancer is a significant health problem. Early diagnosis of the disease is mandatory to increase the effectiveness of the treatment, to augment the chances of cure and to permit conservative surgery. The use of imaging methods is essential in the early diagnosis of the disease. Imaging methods advantages and disadvantages, use and limitations, specificity and sensitivity are presented and discussed. (author)

  6. Pink Ribbons and Red Dresses: A Mixed Methods Content Analysis of Media Coverage of Breast Cancer and Heart Disease. (United States)

    Champion, Claudine; Berry, Tanya R; Kingsley, Bethan; Spence, John C


    This research examined media coverage of breast cancer (n = 145) and heart disease and stroke (n = 39) news articles, videos, advertisements, and images in a local Canadian context through quantitative and thematic content analyses. Quantitative analysis revealed significant differences between coverage of the diseases in placement, survivors as a source of information, health agency, human interest stories, citation of a research study, the inclusion of risk statistics, discussion of preventative behaviors, and tone used. The thematic analysis revealed themes that characterized a "typical" breast cancer survivor and indicated that "good" citizens and businesses should help the cause of breast cancer. Themes for heart disease and stroke articulated individual responsibility and the ways fundraising reinforced femininity and privilege. Findings provide insight on how these diseases are framed in local Canadian media, which might impact an individual's understanding of the disease.

  7. A method for predicting target drug efficiency in cancer based on the analysis of signaling pathway activation. (United States)

    Artemov, Artem; Aliper, Alexander; Korzinkin, Michael; Lezhnina, Ksenia; Jellen, Leslie; Zhukov, Nikolay; Roumiantsev, Sergey; Gaifullin, Nurshat; Zhavoronkov, Alex; Borisov, Nicolas; Buzdin, Anton


    A new generation of anticancer therapeutics called target drugs has quickly developed in the 21st century. These drugs are tailored to inhibit cancer cell growth, proliferation, and viability by specific interactions with one or a few target proteins. However, despite formally known molecular targets for every "target" drug, patient response to treatment remains largely individual and unpredictable. Choosing the most effective personalized treatment remains a major challenge in oncology and is still largely trial and error. Here we present a novel approach for predicting target drug efficacy based on the gene expression signature of the individual tumor sample(s). The enclosed bioinformatic algorithm detects activation of intracellular regulatory pathways in the tumor in comparison to the corresponding normal tissues. According to the nature of the molecular targets of a drug, it predicts whether the drug can prevent cancer growth and survival in each individual case by blocking the abnormally activated tumor-promoting pathways or by reinforcing internal tumor suppressor cascades. To validate the method, we compared the distribution of predicted drug efficacy scores for five drugs (Sorafenib, Bevacizumab, Cetuximab, Sorafenib, Imatinib, Sunitinib) and seven cancer types (Clear Cell Renal Cell Carcinoma, Colon cancer, Lung adenocarcinoma, non-Hodgkin Lymphoma, Thyroid cancer and Sarcoma) with the available clinical trials data for the respective cancer types and drugs. The percent of responders to a drug treatment correlated significantly (Pearson's correlation 0.77 p = 0.023) with the percent of tumors showing high drug scores calculated with the current algorithm.

  8. Comparison of multivariate analysis methods for extracting the paraffin component from the paraffin-embedded cancer tissue spectra for Raman imaging (United States)

    Meksiarun, Phiranuphon; Ishigaki, Mika; Huck-Pezzei, Verena A. C.; Huck, Christian W.; Wongravee, Kanet; Sato, Hidetoshi; Ozaki, Yukihiro


    This study aimed to extract the paraffin component from paraffin-embedded oral cancer tissue spectra using three multivariate analysis (MVA) methods; Independent Component Analysis (ICA), Partial Least Squares (PLS) and Independent Component - Partial Least Square (IC-PLS). The estimated paraffin components were used for removing the contribution of paraffin from the tissue spectra. These three methods were compared in terms of the efficiency of paraffin removal and the ability to retain the tissue information. It was found that ICA, PLS and IC-PLS could remove the paraffin component from the spectra at almost the same level while Principal Component Analysis (PCA) was incapable. In terms of retaining cancer tissue spectral integrity, effects of PLS and IC-PLS on the non-paraffin region were significantly less than that of ICA where cancer tissue spectral areas were deteriorated. The paraffin-removed spectra were used for constructing Raman images of oral cancer tissue and compared with Hematoxylin and Eosin (H&E) stained tissues for verification. This study has demonstrated the capability of Raman spectroscopy together with multivariate analysis methods as a diagnostic tool for the paraffin-embedded tissue section.


    Institute of Scientific and Technical Information of China (English)

    武爱文; 顾晋; 薛钟麒; 王怡; 徐光炜


    To explore the death-related factors of stageⅠrectal cancer patients. Methods: 89 cases of stage I rectal cancer patients between 1985 and 2000 were retrospectively studied for prognostic factors. Factors including age, gender, tumor size, circumferential occupation, gross type, pathological type, depth of tumor invasion, surgical procedure, adjuvant chemotherapy and postoperative complication were chosen for cox multivariate analysis (forward procedure) using Spss software (10.0 version). Results: multivariate analysis demonstrated that muscular invasion was an independent negative prognostic factor for stageⅠrectal cancer patients (P=0.003). Conclusion: Muscular invasion is a negative prognostic factor for stage I rectal cancer patients.

  10. A review and meta-analysis of prospective studies of red and processed meat, meat cooking methods, heme iron, heterocyclic amines and prostate cancer. (United States)

    Bylsma, Lauren C; Alexander, Dominik D


    Prostate cancer remains a significant public health concern among men in the U.S. and worldwide. Epidemiologic studies have generally produced inconclusive results for dietary risk factors for prostate cancer, including consumption of red and processed meats. We aimed to update a previous meta-analysis of prospective cohorts of red and processed meats and prostate cancer with the inclusion of new and updated cohort studies, as well as evaluate meat cooking methods, heme iron, and heterocyclic amine (HCA) intake exposure data. A comprehensive literature search was performed and 26 publications from 19 different cohort studies were included. Random effects models were used to calculate summary relative risk estimates (SRREs) for high vs. low exposure categories. Additionally, meta-regression analyses and stratified intake analyses were conducted to evaluate dose-response relationships. The SRREs for total prostate cancer and total red meat consumption, fresh red meat consumption, and processed meat consumption were 1.02 (95% CI: 0.92-1.12), 1.06 (95% CI: 0.97-1.16), and 1.05 (95% CI: 1.01-1.10), respectively. Analyses were also conducted for the outcomes of non-advanced, advanced, and fatal prostate cancer when sufficient data were available, but these analyses did not produce significant results. No significant SRREs were observed for any of the meat cooking methods, HCA, or heme iron analyses. Dose-response analyses did not reveal significant patterns of associations between red or processed meat and prostate cancer. In conclusion, the results from our analyses do not support an association between red meat or processed consumption and prostate cancer, although we observed a weak positive summary estimate for processed meats.

  11. A novel method for sample preparation of fresh lung cancer tissue for proteomics analysis by tumor cell enrichment and removal of blood contaminants


    Orre Lotta; Bergman Per; Elmberger Göran; Pernemalm Maria; De Petris Luigi; Lewensohn Rolf; Lehtiö Janne


    Abstract Background In-depth proteomics analyses of tumors are frequently biased by the presence of blood components and stromal contamination, which leads to large experimental variation and decreases the proteome coverage. We have established a reproducible method to prepare freshly collected lung tumors for proteomics analysis, aiming at tumor cell enrichment and reduction of plasma protein contamination. We obtained enriched tumor-cell suspensions (ETS) from six lung cancer cases (two ade...

  12. Critical analysis of the images methods in detection and diagnosis in breast cancer; Analise critica dos metodos de imagem na deteccao e diagnostico do cancer mamario

    Energy Technology Data Exchange (ETDEWEB)

    Mendonca, Maria H.S.


    The female breast cancer is a relevant health issue among female population, due its incidence and remarkable effects in the biological, psychological and social levels. Its early diagnosis is important because it allows more effective treatments and enhances changes of cure, even allowing conservative surgical procedures. To make this possible it is essential the periodic breast imaging exams. The available imaging methods to date are: mammography, ultrasonography, thermography, nuclear medicine, computed tomography and MRI. All these methods have their advantages and disadvantages, applications and limitations and some are even in experimental stages. These methods must exercised in association to become more effective. Mammography is still, beyond and doubt the elected breast exam. even though imperfect. It must be performed repeatedly at periodic intervals depending upon the intrinsic conditions of the patient. The other methods complement the mammographic findings, clearing some of them. In this paper, the imaging methods available in our environmental for detected diagnosis of the early breast cancer are analyzed with emphasis in mammography and ultrasonography. Their advantages, disadvantages, indications and limitations are discussed. (author). 205 refs., 12 figs.

  13. Osteolytica: An automated image analysis software package that rapidly measures cancer-induced osteolytic lesions in in vivo models with greater reproducibility compared to other commonly used methods. (United States)

    Evans, H R; Karmakharm, T; Lawson, M A; Walker, R E; Harris, W; Fellows, C; Huggins, I D; Richmond, P; Chantry, A D


    Methods currently used to analyse osteolytic lesions caused by malignancies such as multiple myeloma and metastatic breast cancer vary from basic 2-D X-ray analysis to 2-D images of micro-CT datasets analysed with non-specialised image software such as ImageJ. However, these methods have significant limitations. They do not capture 3-D data, they are time-consuming and they often suffer from inter-user variability. We therefore sought to develop a rapid and reproducible method to analyse 3-D osteolytic lesions in mice with cancer-induced bone disease. To this end, we have developed Osteolytica, an image analysis software method featuring an easy to use, step-by-step interface to measure lytic bone lesions. Osteolytica utilises novel graphics card acceleration (parallel computing) and 3-D rendering to provide rapid reconstruction and analysis of osteolytic lesions. To evaluate the use of Osteolytica we analysed tibial micro-CT datasets from murine models of cancer-induced bone disease and compared the results to those obtained using a standard ImageJ analysis method. Firstly, to assess inter-user variability we deployed four independent researchers to analyse tibial datasets from the U266-NSG murine model of myeloma. Using ImageJ, inter-user variability between the bones was substantial (±19.6%), in contrast to using Osteolytica, which demonstrated minimal variability (±0.5%). Secondly, tibial datasets from U266-bearing NSG mice or BALB/c mice injected with the metastatic breast cancer cell line 4T1 were compared to tibial datasets from aged and sex-matched non-tumour control mice. Analyses by both Osteolytica and ImageJ showed significant increases in bone lesion area in tumour-bearing mice compared to control mice. These results confirm that Osteolytica performs as well as the current 2-D ImageJ osteolytic lesion analysis method. However, Osteolytica is advantageous in that it analyses over the entirety of the bone volume (as opposed to selected 2-D images), it

  14. Sampling in Atypical Endometrial Hyperplasia: Which Method Results in the Lowest Underestimation of Endometrial Cancer? A Systematic Review and Meta-analysis. (United States)

    Bourdel, Nicolas; Chauvet, Pauline; Tognazza, Enrica; Pereira, Bruno; Botchorishvili, Revaz; Canis, Michel


    Our objective was to identify the most accurate method of endometrial sampling for the diagnosis of complex atypical hyperplasia (CAH), and the related risk of underestimation of endometrial cancer. We conducted a systematic literature search in PubMed and EMBASE (January 1999-September 2013) to identify all registered articles on this subject. Studies were selected with a 2-step method. First, titles and abstracts were analyzed by 2 reviewers, and 69 relevant articles were selected for full reading. Then, the full articles were evaluated to determine whether full inclusion criteria were met. We selected 27 studies, taking into consideration the comparison between histology of endometrial hyperplasia obtained by diagnostic tests of interest (uterine curettage, hysteroscopically guided biopsy, or hysteroscopic endometrial resection) and subsequent results of hysterectomy. Analysis of the studies reviewed focused on 1106 patients with a preoperative diagnosis of atypical endometrial hyperplasia. The mean risk of finding endometrial cancer at hysterectomy after atypical endometrial hyperplasia diagnosed by uterine curettage was 32.7% (95% confidence interval [CI], 26.2-39.9), with a risk of 45.3% (95% CI, 32.8-58.5) after hysteroscopically guided biopsy and 5.8% (95% CI, 0.8-31.7) after hysteroscopic resection. In total, the risk of underestimation of endometrial cancer reaches a very high rate in patients with CAH using the classic method of evaluation (i.e., uterine curettage or hysteroscopically guided biopsy). This rate of underdiagnosed endometrial cancer leads to the risk of inappropriate surgical procedures (31.7% of tubal conservation in the data available and no abdominal exploration in 24.6% of the cases). Hysteroscopic resection seems to reduce the risk of underdiagnosed endometrial cancer.

  15. Pathway and network analysis of cancer genomes

    DEFF Research Database (Denmark)

    Creixell, Pau; Reimand, Jueri; Haider, Syed


    Genomic information on tumors from 50 cancer types cataloged by the International Cancer Genome Consortium (ICGC) shows that only a few well-studied driver genes are frequently mutated, in contrast to many infrequently mutated genes that may also contribute to tumor biology. Hence there has been...... large interest in developing pathway and network analysis methods that group genes and illuminate the processes involved. We provide an overview of these analysis techniques and show where they guide mechanistic and translational investigations....

  16. Multiplex RT-PCR method for the analysis of the expression of human sialyltransferases: application to breast cancer cells. (United States)

    Recchi, M A; Harduin-Lepers, A; Boilly-Marer, Y; Verbert, A; Delannoy, P


    In many cases of human cancer, the appearance of hypersialylated glycan structures is related to a precise stage of the disease; this may depend on altered regulation of one or more sialyltransferases genes. Since several distinct sialyltransferase enzymes arising from different unique genes transfer sialic acid residues in the same linkage onto the same acceptor, it is impossible to precisely determine which enzyme is involved in the observed phenotype based on enzymatic assays. We have developed a very sensitive and highly reproducible multiplex reverse transcriptase-polymerase chain reaction technique in order to monitor the expression of four human sialyltransferases genes ST6Gal I, ST3Gal I, ST3Gal III and ST3Gal IV in small cell samples. Multiplex PCR amplification using specific primers for each sialyltransferase and detection of amplification products by polyacrylamide gel electrophoresis is a method that is fast and easy to handle and has proven to be useful for establishing sialyltransferase patterns of expression in breast immortalized cell line HBL100 as well as in breast cancer cell lines MCF-7/6, MCF-7/AZ and MDA.


    Chen, G F; Shi, T P; Wang, B J; Wang, X Y; Zang, Q


    This study aimed to analyze the clinical efficacy of different resections in treating non-muscle-invasive bladder cancer (NMIBC), including partial cystectomy, transurethral resection of bladder tumor (TURBT) and holmium laser resection of bladder tumor. Two hundred and sixteen patients were recruited with NMIBC who were available for follow-up visits in hospital, including 62 cases treated with partial cystectomy, 90 cases treated with TURBT and 64 cases with holmium laser resection. Analysis was made on the cases with tumor relapse in the two years, on operation time, blood loss, time for indwelling urinary catheter, hospital stay and complications after operation. Results were compared to the clinical efficacy of these operation patterns. It was found that the two-year relapse rate for TURBT group, partial cystectomy group and Holmium laser resection group was 41%, 31%, and 33% respectively, and the difference had no statistical significance (p>0.05). Both the TURBT group and holmium laser resection group had shorter operation time, hospital stay and time for indwelling urinary catheter as well as much less blood loss when compared with the partial cystectomy group; the difference had statistical significance (pspasm. Therefore, this study presumes that holmium laser resection and TURBT are much safer and quicker for recovery and obviously superior to the partial cystectomy.


    Institute of Scientific and Technical Information of China (English)

    Wei-nan E; Ping-bing Ming


    The heterogeneous multiscale method gives a general framework for the analysis of multiscale methods. In this paper, we demonstrate this by applying this framework to two canonical problems: The elliptic problem with multiscale coefficients and the quasicontinuum method.

  19. Methods for Cervical Cancer Screening

    Directory of Open Access Journals (Sweden)

    Tatiana Vargas-Revilla


    This article is divided in three sections: the first one focuses on the general impact of cervical cancer has hadin CostaRica, these condsection gathers information about different methodologies used around the world to detect this cancer and the third one makes reference to the current development of the screening devise in Mexico that works as a monitoring system and can used by women without external assistance.

  20. Risk analysis of colorectal cancer incidence by gene expression analysis (United States)

    Shangkuan, Wei-Chuan; Lin, Hung-Che; Chang, Yu-Tien; Jian, Chen-En; Fan, Hueng-Chuen; Chen, Kang-Hua; Liu, Ya-Fang; Hsu, Huan-Ming; Chou, Hsiu-Ling; Yao, Chung-Tay


    Background Colorectal cancer (CRC) is one of the leading cancers worldwide. Several studies have performed microarray data analyses for cancer classification and prognostic analyses. Microarray assays also enable the identification of gene signatures for molecular characterization and treatment prediction. Objective Microarray gene expression data from the online Gene Expression Omnibus (GEO) database were used to to distinguish colorectal cancer from normal colon tissue samples. Methods We collected microarray data from the GEO database to establish colorectal cancer microarray gene expression datasets for a combined analysis. Using the Prediction Analysis for Microarrays (PAM) method and the GSEA MSigDB resource, we analyzed the 14,698 genes that were identified through an examination of their expression values between normal and tumor tissues. Results Ten genes (ABCG2, AQP8, SPIB, CA7, CLDN8, SCNN1B, SLC30A10, CD177, PADI2, and TGFBI) were found to be good indicators of the candidate genes that correlate with CRC. From these selected genes, an average of six significant genes were obtained using the PAM method, with an accuracy rate of 95%. The results demonstrate the potential of utilizing a model with the PAM method for data mining. After a detailed review of the published reports, the results confirmed that the screened candidate genes are good indicators for cancer risk analysis using the PAM method. Conclusions Six genes were selected with 95% accuracy to effectively classify normal and colorectal cancer tissues. We hope that these results will provide the basis for new research projects in clinical practice that aim to rapidly assess colorectal cancer risk using microarray gene expression analysis. PMID:28229027

  1. A simpler method of preprocessing MALDI-TOF MS data for differential biomarker analysis: stem cell and melanoma cancer studies

    Directory of Open Access Journals (Sweden)

    Tong Dong L


    Full Text Available Abstract Introduction Raw spectral data from matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF with MS profiling techniques usually contains complex information not readily providing biological insight into disease. The association of identified features within raw data to a known peptide is extremely difficult. Data preprocessing to remove uncertainty characteristics in the data is normally required before performing any further analysis. This study proposes an alternative yet simple solution to preprocess raw MALDI-TOF-MS data for identification of candidate marker ions. Two in-house MALDI-TOF-MS data sets from two different sample sources (melanoma serum and cord blood plasma are used in our study. Method Raw MS spectral profiles were preprocessed using the proposed approach to identify peak regions in the spectra. The preprocessed data was then analysed using bespoke machine learning algorithms for data reduction and ion selection. Using the selected ions, an ANN-based predictive model was constructed to examine the predictive power of these ions for classification. Results Our model identified 10 candidate marker ions for both data sets. These ion panels achieved over 90% classification accuracy on blind validation data. Receiver operating characteristics analysis was performed and the area under the curve for melanoma and cord blood classifiers was 0.991 and 0.986, respectively. Conclusion The results suggest that our data preprocessing technique removes unwanted characteristics of the raw data, while preserving the predictive components of the data. Ion identification analysis can be carried out using MALDI-TOF-MS data with the proposed data preprocessing technique coupled with bespoke algorithms for data reduction and ion selection.

  2. Cancer detection by quantitative fluorescence image analysis. (United States)

    Parry, W L; Hemstreet, G P


    Quantitative fluorescence image analysis is a rapidly evolving biophysical cytochemical technology with the potential for multiple clinical and basic research applications. We report the application of this technique for bladder cancer detection and discuss its potential usefulness as an adjunct to methods used currently by urologists for the diagnosis and management of bladder cancer. Quantitative fluorescence image analysis is a cytological method that incorporates 2 diagnostic techniques, quantitation of nuclear deoxyribonucleic acid and morphometric analysis, in a single semiautomated system to facilitate the identification of rare events, that is individual cancer cells. When compared to routine cytopathology for detection of bladder cancer in symptomatic patients, quantitative fluorescence image analysis demonstrated greater sensitivity (76 versus 33 per cent) for the detection of low grade transitional cell carcinoma. The specificity of quantitative fluorescence image analysis in a small control group was 94 per cent and with the manual method for quantitation of absolute nuclear fluorescence intensity in the screening of high risk asymptomatic subjects the specificity was 96.7 per cent. The more familiar flow cytometry is another fluorescence technique for measurement of nuclear deoxyribonucleic acid. However, rather than identifying individual cancer cells, flow cytometry identifies cellular pattern distributions, that is the ratio of normal to abnormal cells. Numerous studies by others have shown that flow cytometry is a sensitive method to monitor patients with diagnosed urological disease. Based upon results in separate quantitative fluorescence image analysis and flow cytometry studies, it appears that these 2 fluorescence techniques may be complementary tools for urological screening, diagnosis and management, and that they also may be useful separately or in combination to elucidate the oncogenic process, determine the biological potential of tumors

  3. Analysis of margin index as a method for predicting residual disease after breast-conserving surgery in a European cancer center.

    LENUS (Irish Health Repository)

    Bolger, Jarlath C


    INTRODUCTION: Breast-conserving surgery (BCS), followed by appropriate adjuvant therapies is established as a standard treatment option for women with early-stage invasive breast cancers. A number of factors have been shown to correlate with local and regional disease recurrence. Although margin status is a strong predictor of disease recurrence, consensus is yet to be established on the optimum margin necessary. Margenthaler et al. recently proposed the use of a "margin index," combining tumor size and margin status as a predictor of residual disease after BCS. We applied this new predictive tool to a population of patients with primary breast cancer who presented to a symptomatic breast unit to determine its suitability in predicting those who require reexcision surgery. METHODS: Retrospective analysis of our breast cancer database from January 1, 2000 to June 30, 2010 was performed, including all patients who underwent BCS. Of 531 patients who underwent BCS, 27.1% (144\\/531) required further reexcision procedures, and 55 were eligible for inclusion in the study. Margin index was calculated as: margin index = closest margin (mm)\\/tumor size (mm) x 100, with index >5 considered optimum. RESULTS: Of the 55 patients included, 31% (17\\/55) had residual disease. Fisher\\'s exact test showed margin index not to be a significant predictor of residual disease on reexcision specimen (P = 0.57). Of note, a significantly higher proportion of our patients presented with T2\\/3 tumors (60% vs. 38%). CONCLUSIONS: Although an apparently elegant tool for predicting residual disease after BCS, we have shown that it is not applicable to a symptomatic breast unit in Ireland.

  4. Analysis of Margin Index as a Method for Predicting Residual Disease After Breast-Conserving Surgery in a European Cancer Center.

    LENUS (Irish Health Repository)

    Bolger, Jarlath C


    INTRODUCTION: Breast-conserving surgery (BCS), followed by appropriate adjuvant therapies is established as a standard treatment option for women with early-stage invasive breast cancers. A number of factors have been shown to correlate with local and regional disease recurrence. Although margin status is a strong predictor of disease recurrence, consensus is yet to be established on the optimum margin necessary. Margenthaler et al. recently proposed the use of a "margin index," combining tumor size and margin status as a predictor of residual disease after BCS. We applied this new predictive tool to a population of patients with primary breast cancer who presented to a symptomatic breast unit to determine its suitability in predicting those who require reexcision surgery. METHODS: Retrospective analysis of our breast cancer database from January 1, 2000 to June 30, 2010 was performed, including all patients who underwent BCS. Of 531 patients who underwent BCS, 27.1% (144\\/531) required further reexcision procedures, and 55 were eligible for inclusion in the study. Margin index was calculated as: margin index = closest margin (mm)\\/tumor size (mm) × 100, with index >5 considered optimum. RESULTS: Of the 55 patients included, 31% (17\\/55) had residual disease. Fisher\\'s exact test showed margin index not to be a significant predictor of residual disease on reexcision specimen (P = 0.57). Of note, a significantly higher proportion of our patients presented with T2\\/3 tumors (60% vs. 38%). CONCLUSIONS: Although an apparently elegant tool for predicting residual disease after BCS, we have shown that it is not applicable to a symptomatic breast unit in Ireland.

  5. Evaluation of an effective sample prefractionation method for the proteome analysis of breast cancer tissue using narrow range two-dimensional gel electrophoresis. (United States)

    Lee, KiBeom


    One method of improving the protein profiling of complex mammalian proteomes is the use of prefractionation followed by application of narrow pH range two dimensional (2-D) gels. The success of this strategy relies on sample solubilization; poor solubilization has been associated with missing protein fractions and diffuse, streaked, and/or trailing protein spots. In this study, I sought to optimize the solubilization of prefractionated human cancer cell samples using isoelectric focusing (IEF) rehydration buffers containing a variety of commercially available reducing agents, detergents, chaotropes, and carrier ampholytes. The solubilized proteins were resolved on 2-D gels and compared. Among five tested IEF rehydration buffers, those containing 3-[(3-cholamidopropyl)dimethylamino]-1-propane sulfonate (CHAPS) and dithiothreitol (DTT) provided superior resolution, while that containing Nonidet P-40 (NP-40) did not significantly affect protein resolution, and the tributyl phosphine (TBP)-containing buffer yielded consistently poor results. In addition, I found that buffers containing typically high urea and ampholyte levels generated sharper 2-D gels. Using these optimized conditions, I was able to apply 2-D gel analysis successfully to fractionated proteins from human breast cancer tissue MCF-7, across a pH range of 4-6.7.

  6. Pancreatic Cancer Imaging: Which Method?

    Directory of Open Access Journals (Sweden)

    Santo E


    Full Text Available Pancreatic cancer is the 10th most common malignancy and the 4th largest cancer killer in adults. Surgery offers the only chance of curing these patients. Complete surgical resection is associated with a 5-year survival rate of between 20 and 30%. The challenge is how to best select those patients for curative surgery. Early studies demonstrated excellent sensitivity of EUS in detecting pancreatic tumors in comparison to CT. Similarly, EUS showed an 85-94% accuracy rate for T staging and 70-80% accuracy rate for N staging. Later studies report on substantially less TN staging accuracy for EUS. Possible explanations and the problem of vascular involvement assessment by EUS will be provided. Considering the role of EUS in M staging and a comparison between EUS, MRI, and positron emission tomography, scanning will be presented. A diagnostic algorithm for the evaluation of patients with a suspected pancreatic mass will be offered, stressing the pivotal role of EUS.

  7. A novel method for sample preparation of fresh lung cancer tissue for proteomics analysis by tumor cell enrichment and removal of blood contaminants

    Directory of Open Access Journals (Sweden)

    Orre Lotta


    Full Text Available Abstract Background In-depth proteomics analyses of tumors are frequently biased by the presence of blood components and stromal contamination, which leads to large experimental variation and decreases the proteome coverage. We have established a reproducible method to prepare freshly collected lung tumors for proteomics analysis, aiming at tumor cell enrichment and reduction of plasma protein contamination. We obtained enriched tumor-cell suspensions (ETS from six lung cancer cases (two adenocarcinomas, two squamous-cell carcinomas, two large-cell carcinomas and from two normal lung samples. The cell content of resulting ETS was evaluated with immunocytological stainings and compared with the histologic pattern of the original specimens. By means of a quantitative mass spectrometry-based method we evaluated the reproducibility of the sample preparation protocol and we assessed the proteome coverage by comparing lysates from ETS samples with the direct lysate of corresponding fresh-frozen samples. Results Cytological analyses on cytospin specimens showed that the percentage of tumoral cells in the ETS samples ranged from 20% to 70%. In the normal lung samples the percentage of epithelial cells was less then 10%. The reproducibility of the sample preparation protocol was very good, with coefficient of variation at the peptide level and at the protein level of 13% and 7%, respectively. Proteomics analysis led to the identification of a significantly higher number of proteins in the ETS samples than in the FF samples (244 vs 109, respectively. Albumin and hemoglobin were among the top 5 most abundant proteins identified in the FF samples, showing a high contamination with blood and plasma proteins, whereas ubiquitin and the mitochondrial ATP synthase 5A1 where among the top 5 most abundant proteins in the ETS samples. Conclusion The method is feasible and reproducible. We could obtain a fair enrichment of cells but the major benefit of the method

  8. Methods of Multivariate Analysis

    CERN Document Server

    Rencher, Alvin C


    Praise for the Second Edition "This book is a systematic, well-written, well-organized text on multivariate analysis packed with intuition and insight . . . There is much practical wisdom in this book that is hard to find elsewhere."-IIE Transactions Filled with new and timely content, Methods of Multivariate Analysis, Third Edition provides examples and exercises based on more than sixty real data sets from a wide variety of scientific fields. It takes a "methods" approach to the subject, placing an emphasis on how students and practitioners can employ multivariate analysis in real-life sit

  9. New Method for Early Cancer Diagnosis

    Institute of Scientific and Technical Information of China (English)


    @@ The NSFC funded Key Program project"A real-time analysis of the early diagnosis of cancer mark-ers",undertaken by Changchun Institute of Applied Chemistry,Chinese Academy of Sciences (CAS),re-cently received recognition from an expert team for assessment.Experts pointed out that the research was of great value for the fast ascertain of cancer markers and the early warning and diagnosis.The research team was headed by Academician Wang Erkang,CAS and Prof.Kong Jilie,Fudan University.

  10. Analysis of numerical methods

    CERN Document Server

    Isaacson, Eugene


    This excellent text for advanced undergraduates and graduate students covers norms, numerical solution of linear systems and matrix factoring, iterative solutions of nonlinear equations, eigenvalues and eigenvectors, polynomial approximation, and other topics. It offers a careful analysis and stresses techniques for developing new methods, plus many examples and problems. 1966 edition.

  11. Sparse discriminant analysis for breast cancer biomarker identification and classification

    Institute of Scientific and Technical Information of China (English)

    Yu Shi; Daoqing Dai; Chaochun Liu; Hong Yan


    Biomarker identification and cancer classification are two important procedures in microarray data analysis. We propose a novel uni-fied method to carry out both tasks. We first preselect biomarker candidates by eliminating unrelated genes through the BSS/WSS ratio filter to reduce computational cost, and then use a sparse discriminant analysis method for simultaneous biomarker identification and cancer classification. Moreover, we give a mathematical justification about automatic biomarker identification. Experimental results show that the proposed method can identify key genes that have been verified in biochemical or biomedical research and classify the breast cancer type correctly.

  12. Comparative genomic analysis of esophageal cancers. (United States)

    Caygill, Christine P J; Gatenby, Piers A C; Herceg, Zdenko; Lima, Sheila C S; Pinto, Luis F R; Watson, Anthony; Wu, Ming-Shiang


    The following, from the 12th OESO World Conference: Cancers of the Esophagus, includes commentaries on comparative genomic analysis of esophageal cancers: genomic polymorphisms, the genetic and epigenetic drivers in esophageal cancers, and the collection of data in the UK Barrett's Oesophagus Registry.

  13. Review and research analysis of computational target methods using BioRuby and in silico screening of herbal lead compounds against pancreatic cancer using R programming. (United States)

    Jayadeepa, R M; Ray, Ankita; Naik, Dhaval; Sanyal, Debendra Nath; Shah, Disha


    Plants and their natural components sophisticated with the cornerstone of traditional conventional medicinal system throughout the globe for many years and extend to furnish mankind with latest remedies. Natural Products act as lead molecules for the synthesis of various potent drugs. In the current research a study is conducted on herbal small molecule and their potential binding chemical affinity to the effect or molecules of major diseases such as pancreatic cancer. Clinical studies demonstrate correlation between Cyclin- Dependent Kinase 4 (CDK4) and malignant progression of Pancreatic Cancer. Using Bioruby Gem's we were able to analyze better characteristics of the target protein. VegaZZ and NAMD were used to minimize the energy of the target protein. Therefore identification of effective, well- tolerated targets was analyzed. Further the target protein was subjected to docking with the anti cancer inhibitors which represents a rational chemo preventive strategy using AutoDock Vina. Later using the dock score top ranked phytochemicals were analyzed for Toxicity Analysis. Using the BioRuby gem we were able to measure the distance between the amino acid. Various R scripting libraries were used to hunt the best leads, as in this case the phytochemicals. Phytochemicals such as Wedelolactones and Catechin were analyzed computationally. This study has presented the various effects of naturally occurring anti pancreatic cancer compounds Catechin, Wedelolactones that inhibits Cyclin Dependent Kinase 4. The study results reveal that compounds use less binding energy to CDK4 and inhibit its activity. Future investigation of other various wet lab studies such as cell line studies will confirm results of these two herbal chemical formulations potential ones for treating Pancreatic Cancer.

  14. Coupled Two-Way Clustering Analysis of Breast Cancer and Colon Cancer Gene Expression Data

    CERN Document Server

    Getz, G; Kela, I; Domany, E; Notterman, D A; Getz, Gad; Gal, Hilah; Kela, Itai; Domany, Eytan; Notterman, Dan A.


    We present and review Coupled Two Way Clustering, a method designed to mine gene expression data. The method identifies submatrices of the total expression matrix, whose clustering analysis reveals partitions of samples (and genes) into biologically relevant classes. We demonstrate, on data from colon and breast cancer, that we are able to identify partitions that elude standard clustering analysis.

  15. Methods for RNA Analysis

    DEFF Research Database (Denmark)

    Olivarius, Signe

    While increasing evidence appoints diverse types of RNA as key players in the regulatory networks underlying cellular differentiation and metabolism, the potential functions of thousands of conserved RNA structures encoded in mammalian genomes remain to be determined. Since the functions of most...... RNAs rely on interactions with proteins, the establishment of protein-binding profiles is essential for the characterization of RNAs. Aiming to facilitate RNA analysis, this thesis introduces proteomics- as well as transcriptomics-based methods for the functional characterization of RNA. First, RNA......-protein pulldown combined with mass spectrometry analysis is applied for in vivo as well as in vitro identification of RNA-binding proteins, the latter succeeding in verifying known RNA-protein interactions. Secondly, acknowledging the significance of flexible promoter usage for the diversification...

  16. Microfluidics and cancer analysis: cell separation, cell/tissue culture, cell mechanics, and integrated analysis systems. (United States)

    Pappas, Dimitri


    Among the growing number of tools available for cancer studies, microfluidic systems have emerged as a promising analytical tool to elucidate cancer cell and tumor function. Microfluidic methods to culture cells have created approaches to provide a range of environments from single-cell analysis to complex three-dimensional devices. In this review we discuss recent advances in tumor cell culture, cancer cell analysis, and advanced studies enabled by microfluidic systems.

  17. Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues. (United States)

    Hwang, S-I; Thumar, J; Lundgren, D H; Rezaul, K; Mayya, V; Wu, L; Eng, J; Wright, M E; Han, D K


    Successful treatment of multiple cancer types requires early detection and identification of reliable biomarkers present in specific cancer tissues. To test the feasibility of identifying proteins from archival cancer tissues, we have developed a methodology, termed direct tissue proteomics (DTP), which can be used to identify proteins directly from formalin-fixed paraffin-embedded prostate cancer tissue samples. Using minute prostate biopsy sections, we demonstrate the identification of 428 prostate-expressed proteins using the shotgun method. Because the DTP method is not quantitative, we employed the absolute quantification method and demonstrate picogram level quantification of prostate-specific antigen. In depth bioinformatics analysis of these expressed proteins affords the categorization of metabolic pathways that may be important for distinct stages of prostate carcinogenesis. Furthermore, we validate Wnt-3 as an upregulated protein in cancerous prostate cells by immunohistochemistry. We propose that this general strategy provides a roadmap for successful identification of critical molecular targets of multiple cancer types.


    Institute of Scientific and Technical Information of China (English)

    CHEN Jian-guo; Sankaranarayanan R; SHEN Zhuo-cai; Black RJ; YAO Hong-yu; LI Wen-guang; Parkin DM


    Objective: 16,922 patients with cancers from 15 sites of Qidong population-based cancer registry in the period of 1982-1991 were analyzed for evaluation of cancer survival as well as different cancer control measures.Methods: Observed survival rate (OS) was computed by the Kaplan-Meier method using EGRET statistical software package. Relative survival (RS) which is the ratio of the OS to the expected rate was calculated by using Qidong life table with respect to sex, age and calendar period of observation. Results: The five-year OS for the 5 leading sites of cancers, liver, stomach, lung,oesophagus, and rectum were 1.8%, 11.6%, 3.0% 3.3%,and 19.9%, respectively. The five-year RS for the 5 sites were 1.9%, 14.0%, 3.6%, 4.2%, and 23.7%, respectively,in which, 1.7%, 14.8%, 3.4%, 4.2%, and 26.0% for males, and 2.7%, 12.7%, 4.1%, 4.0%, and 22.0% for females, respectively. Female patients with breast cancer and cervix cancer had 5-year RS of 54.6% and 33.0%.Conclusion: Cancer survival rates for all sites are poor,in which that of the liver is the lowest, while that of the breast, the highest. The survivals of cancers for all sites,especially for breast, cervix, and leukemia are seen to be lower than those of European countries except for oesophagus, pancreas and lung cancer which do not achieve improved survival both in developing and developed countries. There will be a long way to improve the total cancer survival, as well as the cancer treatment in the developing countries.

  19. Optical spectra analysis for breast cancer diagnostics (United States)

    Belkov, S. A.; Kochemasov, G. G.; Lyubynskaya, T. E.; Maslov, N. V.; Nuzhny, A. S.; da Silva, L. B.; Rubenchik, A.


    Minimally invasive probe and optical biopsy system based on optical spectra recording and analysis seem to be a promising tool for early diagnostics of breast cancer. Light scattering and absorption spectra are generated continuously as far as the needle-like probe with one emitting and several collecting optical fibers penetrates through the tissues toward to the suspicious area. That allows analyzing not only the state of local site, but also the structure of tissues along the needle trace. The suggested method has the advantages of automated on-line diagnosing and minimal tissue destruction and in parallel with the conventional diagnostic procedures provides the ground for decision-making. 165 medical trials were completed in Nizhny Novgorod Regional Oncology Centre, Russia. Independent diagnoses were the results of fine biopsy and histology. Application of wavelet expansion and clasterization techniques for spectra analysis revealed several main spectral types for malignant and benign tumors. Automatic classification algorithm demonstrated specificity ˜90% and sensitivity ˜91%. Large amount of information, fuzziness in criteria and data noisiness make neural networks to be an attractive analytic tool. The model based on three-layer perceptron was tested over the sample of 29 `cancer' and 29 `non-cancer' cases and demonstrated total separation.

  20. Internet cancer support groups: a feminist analysis. (United States)

    Im, Eun-Ok; Chee, Wonshik; Tsai, Hsiu-Min; Lin, Li-Chen; Cheng, Ching-Yu


    Internet Cancer Support Groups (ICSGs) are an emerging form of support group on Internet specifically for cancer patients. Previous studies have indicated the effectiveness of ICSGs as a research setting or a data-collection method. Yet recent studies have also indicated that ICSGs tend to serve highly educated, high-income White males who tend to be at an early stage of cancer. In this article, a total of 317 general ICSGs and 229 ethnic-specific ICSGs searched through,,,, and are analyzed from a feminist perspective. The written records of group discussions and written memos by the research staff members were also analyzed using content analysis. The idea categories that emerged about these groups include (a) authenticity issues; (b) ethnicity and gender issues; (c) intersubjectivity issues; and (d) potential ethical issues. The findings suggest that (a) researchers adopt multiple recruitment strategies through various Internet sites and/or real settings; (b) researchers raise their own awareness of the potential influences of the health-related resources provided by ICSGs and regularly update their knowledge related to the federal and state standards and/or policies related to ICSGs; and (c) researchers consider adopting a quota-sampling method.

  1. Comparative effects of different enteral feeding methods in head and neck cancer patients receiving radiotherapy or chemoradiotherapy: a network meta-analysis

    Directory of Open Access Journals (Sweden)

    Zhang ZH


    Full Text Available Zhihong Zhang,1,2 Yu Zhu,1 Yun Ling,3 Lijuan Zhang,1 Hongwei Wan1 1Department of Nursing, Shanghai Proton and Heavy Ion Center, 2Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, 3Department of Human Resource, Shanghai Proton and Heavy Ion Center, Shanghai, People’s Republic of China Abstract: Nasogastric tube (NGT and percutaneous endoscopic gastrostomy were frequently used in the head and neck cancer patients when malnutrition was present. Nevertheless, the evidence was inclusive in terms of the choice and the time of tube placement. The aim of this network meta-analysis was to evaluate the comparative effects of prophylactic percutaneous endoscopic gastrostomy (pPEG, reactive percutaneous endoscopic gastrostomy (rPEG, and NGT in the head and neck cancer patients receiving radiotherapy or chemoradiotherapy. Databases of PubMed, Web of Science, and Elsevier were searched from inception to October 2015. Thirteen studies enrolling 1,631 participants were included in this network meta-analysis. The results indicated that both pPEG and NGT were superior to rPEG in the management of weight loss. pPEG was associated with the least rate of treatment interruption and nutrition-related hospital admission among pPEG, rPEG, and NGT. Meanwhile, there was no difference in tube-related complications. Our study suggested that pPEG might be a better choice in malnutrition management in the head and neck cancer patients undergoing radiotherapy or chemoradiotherapy. However, its effects need to be further investigated in more randomized controlled trials. Keywords: malnutrition, tube feeding, weight loss, treatment interruption, readmission, complication

  2. Cancer incidence in men: a cluster analysis of spatial patterns

    Directory of Open Access Journals (Sweden)

    D'Alò Daniela


    Full Text Available Abstract Background Spatial clustering of different diseases has received much less attention than single disease mapping. Besides chance or artifact, clustering of different cancers in a given area may depend on exposure to a shared risk factor or to multiple correlated factors (e.g. cigarette smoking and obesity in a deprived area. Models developed so far to investigate co-occurrence of diseases are not well-suited for analyzing many cancers simultaneously. In this paper we propose a simple two-step exploratory method for screening clusters of different cancers in a population. Methods Cancer incidence data were derived from the regional cancer registry of Umbria, Italy. A cluster analysis was performed on smoothed and non-smoothed standardized incidence ratios (SIRs of the 13 most frequent cancers in males. The Besag, York and Mollie model (BYM and Poisson kriging were used to produce smoothed SIRs. Results Cluster analysis on non-smoothed SIRs was poorly informative in terms of clustering of different cancers, as only larynx and oral cavity were grouped, and of characteristic patterns of cancer incidence in specific geographical areas. On the other hand BYM and Poisson kriging gave similar results, showing cancers of the oral cavity, larynx, esophagus, stomach and liver formed a main cluster. Lung and urinary bladder cancers clustered together but not with the cancers mentioned above. Both methods, particularly the BYM model, identified distinct geographic clusters of adjacent areas. Conclusion As in single disease mapping, non-smoothed SIRs do not provide reliable estimates of cancer risks because of small area variability. The BYM model produces smooth risk surfaces which, when entered into a cluster analysis, identify well-defined geographical clusters of adjacent areas. It probably enhances or amplifies the signal arising from exposure of more areas (statistical units to shared risk factors that are associated with different cancers. In

  3. Meta analysis of risk factors for colorectal cancer

    Institute of Scientific and Technical Information of China (English)

    Kun Chen; Jiong-Liang Qiu; Yang Zhang; Yu-Wan Zhao


    AIM: To study the risk factors for colorectal cancer in China.METHODS: A meta-analysis of the risk factors of colorectal cancer was conducted for 14 case-control studies, and reviewed 14 reports within 13 years which included 5034cases and 5205 controls. Dersimonian and Laird random effective models were used to process the results.RESULTS: Meta analysis of the 14 studies demonstrated that proper physical activites and dietary fibers were protective factors (pooled OR<0.8), while fecal mucohemorrhage,chronic diarrhea and polyposis were highly associated with colorectal cancer (all pooled OR>4). The stratified results showed that different OR values of some factors were due to geographic factors or different resourses.CONCLUSION: Risks of colorectal cancer are significantly associated with the histories of intestinal diseases or relative symptoms, high lipid diet, emotional trauma and family history of cancers. The suitable physical activities and dietary fibers are protective factors.

  4. A comparison of Ki-67 counting methods in luminal Breast Cancer: The Average Method vs. the Hot Spot Method (United States)

    Jang, Min Hye; Kim, Hyun Jung; Chung, Yul Ri; Lee, Yangkyu


    In spite of the usefulness of the Ki-67 labeling index (LI) as a prognostic and predictive marker in breast cancer, its clinical application remains limited due to variability in its measurement and the absence of a standard method of interpretation. This study was designed to compare the two methods of assessing Ki-67 LI: the average method vs. the hot spot method and thus to determine which method is more appropriate in predicting prognosis of luminal/HER2-negative breast cancers. Ki-67 LIs were calculated by direct counting of three representative areas of 493 luminal/HER2-negative breast cancers using the two methods. We calculated the differences in the Ki-67 LIs (ΔKi-67) between the two methods and the ratio of the Ki-67 LIs (H/A ratio) of the two methods. In addition, we compared the performance of the Ki-67 LIs obtained by the two methods as prognostic markers. ΔKi-67 ranged from 0.01% to 33.3% and the H/A ratio ranged from 1.0 to 2.6. Based on the receiver operating characteristic curve method, the predictive powers of the KI-67 LI measured by the two methods were similar (Area under curve: hot spot method, 0.711; average method, 0.700). In multivariate analysis, high Ki-67 LI based on either method was an independent poor prognostic factor, along with high T stage and node metastasis. However, in repeated counts, the hot spot method did not consistently classify tumors into high vs. low Ki-67 LI groups. In conclusion, both the average and hot spot method of evaluating Ki-67 LI have good predictive performances for tumor recurrence in luminal/HER2-negative breast cancers. However, we recommend using the average method for the present because of its greater reproducibility. PMID:28187177

  5. Predicting response before initiation of neoadjuvant chemotherapy in breast cancer using new methods for the analysis of dynamic contrast enhanced MRI (DCE MRI) data (United States)

    DeGrandchamp, Joseph B.; Whisenant, Jennifer G.; Arlinghaus, Lori R.; Abramson, V. G.; Yankeelov, Thomas E.; Cárdenas-Rodríguez, Julio


    The pharmacokinetic parameters derived from dynamic contrast enhanced (DCE) MRI have shown promise as biomarkers for tumor response to therapy. However, standard methods of analyzing DCE MRI data (Tofts model) require high temporal resolution, high signal-to-noise ratio (SNR), and the Arterial Input Function (AIF). Such models produce reliable biomarkers of response only when a therapy has a large effect on the parameters. We recently reported a method that solves the limitations, the Linear Reference Region Model (LRRM). Similar to other reference region models, the LRRM needs no AIF. Additionally, the LRRM is more accurate and precise than standard methods at low SNR and slow temporal resolution, suggesting LRRM-derived biomarkers could be better predictors. Here, the LRRM, Non-linear Reference Region Model (NRRM), Linear Tofts model (LTM), and Non-linear Tofts Model (NLTM) were used to estimate the RKtrans between muscle and tumor (or the Ktrans for Tofts) and the tumor kep,TOI for 39 breast cancer patients who received neoadjuvant chemotherapy (NAC). These parameters and the receptor statuses of each patient were used to construct cross-validated predictive models to classify patients as complete pathological responders (pCR) or non-complete pathological responders (non-pCR) to NAC. Model performance was evaluated using area under the ROC curve (AUC). The AUC for receptor status alone was 0.62, while the best performance using predictors from the LRRM, NRRM, LTM, and NLTM were AUCs of 0.79, 0.55, 0.60, and 0.59 respectively. This suggests that the LRRM can be used to predict response to NAC in breast cancer.

  6. Noninvasive detection of lung cancer by analysis of exhaled breath

    Directory of Open Access Journals (Sweden)

    Denz Hubert


    Full Text Available Abstract Background Lung cancer is one of the leading causes of death in Europe and the western world. At present, diagnosis of lung cancer very often happens late in the course of the disease since inexpensive, non-invasive and sufficiently sensitive and specific screening methods are not available. Even though the CT diagnostic methods are good, it must be assured that "screening benefit outweighs risk, across all individuals screened, not only those with lung cancer". An early non-invasive diagnosis of lung cancer would improve prognosis and enlarge treatment options. Analysis of exhaled breath would be an ideal diagnostic method, since it is non-invasive and totally painless. Methods Exhaled breath and inhaled room air samples were analyzed using proton transfer reaction mass spectrometry (PTR-MS and solid phase microextraction with subsequent gas chromatography mass spectrometry (SPME-GCMS. For the PTR-MS measurements, 220 lung cancer patients and 441 healthy volunteers were recruited. For the GCMS measurements, we collected samples from 65 lung cancer patients and 31 healthy volunteers. Lung cancer patients were in different disease stages and under treatment with different regimes. Mixed expiratory and indoor air samples were collected in Tedlar bags, and either analyzed directly by PTR-MS or transferred to glass vials and analyzed by gas chromatography mass spectrometry (GCMS. Only those measurements of compounds were considered, which showed at least a 15% higher concentration in exhaled breath than in indoor air. Compounds related to smoking behavior such as acetonitrile and benzene were not used to differentiate between lung cancer patients and healthy volunteers. Results Isoprene, acetone and methanol are compounds appearing in everybody's exhaled breath. These three main compounds of exhaled breath show slightly lower concentrations in lung cancer patients as compared to healthy volunteers (p Conclusion GCMS-SPME is a relatively

  7. An analysis of appropriate delivery of postoperative radiation therapy for endometrial cancer using the RAND/UCLA Appropriateness Method: Executive summary

    Directory of Open Access Journals (Sweden)

    Ellen Jones, MD, PhD


    Conclusions: This analysis based on the RAND/UCLA Method shows significant agreement with the 2014 endometrial Guideline. Areas of divergence, often in scenarios with low-level evidence, included use of external beam RT plus vaginal brachytherapy in stages II and III and external beam RT alone in early-stage patients. Furthermore, the analysis explores other important questions regarding management of this disease site.

  8. A novel meta-analysis approach of cancer transcriptomes reveals prevailing transcriptional networks in cancer cells. (United States)

    Niida, Atsushi; Imoto, Seiya; Nagasaki, Masao; Yamaguchi, Rui; Miyano, Satoru


    Although microarray technology has revealed transcriptomic diversities underlining various cancer phenotypes, transcriptional programs controlling them have not been well elucidated. To decode transcriptional programs governing cancer transcriptomes, we have recently developed a computational method termed EEM, which searches for expression modules from prescribed gene sets defined by prior biological knowledge like TF binding motifs. In this paper, we extend our EEM approach to predict cancer transcriptional networks. Starting from functional TF binding motifs and expression modules identified by EEM, we predict cancer transcriptional networks containing regulatory TFs, associated GO terms, and interactions between TF binding motifs. To systematically analyze transcriptional programs in broad types of cancer, we applied our EEM-based network prediction method to 122 microarray datasets collected from public databases. The data sets contain about 15000 experiments for tumor samples of various tissue origins including breast, colon, lung etc. This EEM based meta-analysis successfully revealed a prevailing cancer transcriptional network which functions in a large fraction of cancer transcriptomes; they include cell-cycle and immune related sub-networks. This study demonstrates broad applicability of EEM, and opens a way to comprehensive understanding of transcriptional networks in cancer cells.

  9. Methods in algorithmic analysis

    CERN Document Server

    Dobrushkin, Vladimir A


    …helpful to any mathematics student who wishes to acquire a background in classical probability and analysis … This is a remarkably beautiful book that would be a pleasure for a student to read, or for a teacher to make into a year's course.-Harvey Cohn, Computing Reviews, May 2010

  10. Pyrosequencing Analysis for Breast Cancer DNA Methylome. (United States)

    Kuscu, Cem; Kuscu, Canan


    Unraveling DNA methylation profile of tumor is important for the diagnosis and treatment of cancer patients. Because of the heterogeneity of clinical samples, it is very difficult to get methylation profile of only tumor cells. Laser capture Microdissection (LCM) is giving us a chance to isolate the DNA only from the tumor cells without any stroma cell's DNA contamination. Once we capture the breast tumor cells, we can isolate the genomic DNA which is followed by the bisulfite treatment in which unmethylated cytosines of the CG pairs are converted into uracil; however, methylated cytosine does not go into any chemical change during this reaction. Next, bisulfite treated DNA is used in the regular PCR reaction to get a single band PCR amplicon which will be used as a template for the pyrosequencing. Pyrosequencing is a powerful method to make a quantitative methylation analysis for each specific CG pair.

  11. Differential network analysis in human cancer research. (United States)

    Gill, Ryan; Datta, Somnath; Datta, Susmita


    A complex disease like cancer is hardly caused by one gene or one protein singly. It is usually caused by the perturbation of the network formed by several genes or proteins. In the last decade several research teams have attempted to construct interaction maps of genes and proteins either experimentally or reverse engineer interaction maps using computational techniques. These networks were usually created under a certain condition such as an environmental condition, a particular disease, or a specific tissue type. Lately, however, there has been greater emphasis on finding the differential structure of the existing network topology under a novel condition or disease status to elucidate the perturbation in a biological system. In this review/tutorial article we briefly mention some of the research done in this area; we mainly illustrate the computational/statistical methods developed by our team in recent years for differential network analysis using publicly available gene expression data collected from a well known cancer study. This data includes a group of patients with acute lymphoblastic leukemia and a group with acute myeloid leukemia. In particular, we describe the statistical tests to detect the change in the network topology based on connectivity scores which measure the association or interaction between pairs of genes. The tests under various scores are applied to this data set to perform a differential network analysis on gene expression for human leukemia. We believe that, in the future, differential network analysis will be a standard way to view the changes in gene expression and protein expression data globally and these types of tests could be useful in analyzing the complex differential signatures.

  12. DNA Double-Strand Break Analysis by {gamma}-H2AX Foci: A Useful Method for Determining the Overreactors to Radiation-Induced Acute Reactions Among Head-and-Neck Cancer Patients

    Energy Technology Data Exchange (ETDEWEB)

    Goutham, Hassan Venkatesh; Mumbrekar, Kamalesh Dattaram [Division of Radiobiology and Toxicology, Manipal Life Sciences Centre, Manipal University, Manipal, Karnataka (India); Vadhiraja, Bejadi Manjunath [Manipal Hospital, Bangalore, Karnataka (India); Fernandes, Donald Jerard; Sharan, Krishna [Department of Radiotherapy and Oncology, Shiridi Sai Baba Cancer Hospital and Research Centre, Kasturba Hospital, Manipal, Karnataka (India); Kanive Parashiva, Guruprasad; Kapaettu, Satyamoorthy [Division of Biotechnology, Manipal Life Sciences Centre, Manipal University, Manipal, Karnataka (India); Bola Sadashiva, Satish Rao, E-mail: [Division of Radiobiology and Toxicology, Manipal Life Sciences Centre, Manipal University, Manipal, Karnataka (India)


    Purpose: Interindividual variability in normal tissue toxicity during radiation therapy is a limiting factor for successful treatment. Predicting the risk of developing acute reactions before initiation of radiation therapy may have the benefit of opting for altered radiation therapy regimens to achieve minimal adverse effects with improved tumor cure. Methods and Materials: DNA double-strand break (DSB) induction and its repair kinetics in lymphocytes of head-and-neck cancer patients undergoing chemoradiation therapy was analyzed by counting {gamma}-H2AX foci, neutral comet assay, and a modified version of neutral filter elution assay. Acute normal tissue reactions were assessed by Radiation Therapy Oncology Group criteria. Results: The correlation between residual DSBs and the severity of acute reactions demonstrated that residual {gamma}-H2AX foci in head-and-neck cancer patients increased with the severity of oral mucositis and skin reaction. Conclusions: Our results suggest that {gamma}-H2AX analysis may have predictive implications for identifying the overreactors to mucositis and skin reactions among head-and-neck cancer patients prior to initiation of radiation therapy.

  13. Method for detecting the presence of prostate cancer (United States)

    Karin, Michael; Luo, Jun-Li; Tan, Wei


    The present invention relates to compositions and methods for cancer diagnosis, treatment and drug screening. In particular, the present invention provides compositions and methods for targeting the nuclear translocation of IkB kinase-.alpha. (IKK.alpha.) and the IKK.alpha.-mediated suppression of Maspin expression observed in metastatic prostate cancer cells.

  14. Stiffness of cancer cells measured with an AFM indentation method. (United States)

    Hayashi, Kozaburo; Iwata, Mayumi


    The stiffness of cancer cells and its changes during metastasis are very important for understanding the pathophysiology of cancer cells and the mechanisms of metastasis of cancer. As the first step of the studies on the mechanics of cancer cells during metastasis, we determined the elasticity and stiffness of cancer cells with an indentation method using an atomic force microscope (AFM), and compared with those of normal cells. In most of the past AFM studies, Young׳s elastic moduli of cells have been calculated from force-indentation data using Hertzian model. As this model is based on several important assumptions including infinitesimal strain and Hooke׳s linear stress-strain law, in the exact sense it cannot be applied to cells that deform very largely and nonlinearly. To overcome this problem, we previously proposed an equation F=a[exp(bδ)-1] to describe relations between force (F) and indentation (δ), where a and b are parameters relating with cellular stiffness. In the present study, we applied this method to cancer cells instead of Young׳s elastic modulus. The conclusions obtained are: 1) AFM indentation test data of cancer cells can be very well described by the above equation, 2) cancer cells are softer than normal cells, and 3) there are no significant locational differences in the stiffness of cancer cells between the central and the peripheral regions. These methods and results are useful for studying the mechanics of cancer cells and the mechanisms of metastasis.

  15. Integrated proteomic analysis of human cancer cells and plasma from tumor bearing mice for ovarian cancer biomarker discovery.

    Directory of Open Access Journals (Sweden)

    Sharon J Pitteri

    Full Text Available The complexity of the human plasma proteome represents a substantial challenge for biomarker discovery. Proteomic analysis of genetically engineered mouse models of cancer and isolated cancer cells and cell lines provide alternative methods for identification of potential cancer markers that would be detectable in human blood using sensitive assays. The goal of this work is to evaluate the utility of an integrative strategy using these two approaches for biomarker discovery.We investigated a strategy that combined quantitative plasma proteomics of an ovarian cancer mouse model with analysis of proteins secreted or shed by human ovarian cancer cells. Of 106 plasma proteins identified with increased levels in tumor bearing mice, 58 were also secreted or shed from ovarian cancer cells. The remainder consisted primarily of host-response proteins. Of 25 proteins identified in the study that were assayed, 8 mostly secreted proteins common to mouse plasma and human cancer cells were significantly upregulated in a set of plasmas from ovarian cancer patients. Five of the eight proteins were confirmed to be upregulated in a second independent set of ovarian cancer plasmas, including in early stage disease.Integrated proteomic analysis of cancer mouse models and human cancer cell populations provides an effective approach to identify potential circulating protein biomarkers.

  16. Hormonally induced modulation in the phosphate metabolites of breast cancer: analysis of in vivo 31P MRS signals with a modified prony method. (United States)

    Viti, V; Ragona, R; Guidoni, L; Barone, P; Furman, E; Degani, H


    A modified Prony method (MPM) was applied to analyze the main signals present in spatially resolved 31P NMR spectra of MCF7 breast tumors implanted in nude mice. First, the method was tested on synthetic data to establish its limits of reliability. Its performance with respect to peak identification and quantification of signal intensities was then exploited on data from three implanted tumors during hormonal manipulation with estrogen and the antiestrogenic drug tamoxifen. The phosphomonoester peak was resolved into phosphocholine (PC) and phosphoethanolamine (PE). Treatment with tamoxifen led to a significant reduction in the PE to PE+PC peak amplitude ratio in the tumors under consideration. MPM analysis also revealed the presence of two different inorganic phosphate pools: a larger acidic pool and a smaller alkaline pool during estrogen-induced growth and the reverse during tumor regression.

  17. Circulating tumor cells in lung cancer: detection methods and clinical applications. (United States)

    Yu, Na; Zhou, Jia; Cui, Fang; Tang, Xiaokui


    Circulating tumor cells (CTCs) are tumor cells that have disseminated from primary and metastatic sites, and circulate in the bloodstream. Advanced immunological and molecular-based methods can be used to detect and analyze the cells with the characteristics of tumor cells, and can be detected and analyzed in the blood of cancer patients. The most commonly used methods in lung cancer combine the processes of immunomagnetic enrichment and immunocytochemical detection, morphology-based enrichment coupled with reverse transcriptase polymerase chain reaction (RT-PCR), and RT-PCR alone. CTC analysis is considered a liquid biopsy approach for early diagnosis, risk stratification, evaluation of curative efficacy, and early detection of lung cancer relapse. In this review, we discuss the present techniques for analyzing CTCs, and the restrictions of using these methods in lung cancer. We also review the clinical studies in lung cancer and discuss the underlying associations between these studies and their future applications to this disease.

  18. Compositions and methods for cancer treatment using targeted carbon nanotubes (United States)

    Harrison, Jr., Roger G; Resasco, Daniel E; Neves, Luis Filipe Ferreira


    The present invention is a method for detecting and destroying cancer tumors. The method is based on the concept of associating a linking protein or linking peptide such as, but not limited to, annexin V or other annexins to carbon nanotubes such as single-walled carbon nanotubes (SWNTs) to form a protein-CNT complex. Said linking protein or peptide can selectively bind to cancerous cells, especially tumor vasculature endothelial cells, rather than to healthy ones by binding to cancer-specific external receptors such as anionic phospholipids including phosphatidylserine expressed on the outer surfaces of cancer cells only. Irradiation of bound CNTs with one or more specific electromagnetic wavelengths is then used to detect and destroy those cells to which the CNTs are bound via the linking protein or peptide thereby destroying the tumor or cancer cells and preferably an immunostimulant is provided to the patient to enhance the immune response against antigens released from the tumor or cancer cells.

  19. Breast Image Analysis for Risk Assessment, Detection, Diagnosis, and Treatment of Cancer

    NARCIS (Netherlands)

    Giger, M.L.; Karssemeijer, N.; Schnabel, J.A.


    The role of breast image analysis in radiologists' interpretation tasks in cancer risk assessment, detection, diagnosis, and treatment continues to expand. Breast image analysis methods include segmentation, feature extraction techniques, classifier design, biomechanical modeling, image registration

  20. Probabilistic methods for rotordynamics analysis (United States)

    Wu, Y.-T.; Torng, T. Y.; Millwater, H. R.; Fossum, A. F.; Rheinfurth, M. H.


    This paper summarizes the development of the methods and a computer program to compute the probability of instability of dynamic systems that can be represented by a system of second-order ordinary linear differential equations. Two instability criteria based upon the eigenvalues or Routh-Hurwitz test functions are investigated. Computational methods based on a fast probability integration concept and an efficient adaptive importance sampling method are proposed to perform efficient probabilistic analysis. A numerical example is provided to demonstrate the methods.

  1. Tools for building Breast Cancer CAD methods; Herramientas para elaborar metodos de CAD del cancer de mama

    Energy Technology Data Exchange (ETDEWEB)

    Diaz-Herrero, G.; Franco-Valiente, J. M.; Suarez-Ortega, C.; Rubio del Solar, M.; Ramos-Pollam, R.; Guevara-Lopez, M. A.; Gonzalez de Posada, N.; Ramos, I.; Loureiro, J.


    This paper describes the main results of the collaboration currently ongoing between CETA-CIEMAT and the Faculty of Engineering at the University of Porto. It introduces the Mammography image Workstation for Analysis and Diagnosis (MIWAD) and the data analysis processes through which Grid infrastructures are used to develop Breast Cancer Computer-Aided Diagnosis (CAD) methods.MIWAD is a novel integrated software framework that integrates a specialized graphical user interface combining digital image processing, pattern recognition and artificial intelligence techniques. This paper describes its successful application in a pilot experience, on the first Portuguese Breast Cancer Digital Repository. (Author)

  2. Compositions and methods for cancer treatment using targeted carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Harrison, Jr., Roger G.; Resasco, Daniel E.; Neves, Luis Filipe Ferreira


    Compositions for detecting and/or destroying cancer tumors and/or cancer cells via photodynamic therapy are disclosed, as well as methods of use thereof. The compositions comprise a linking protein or peptide attached to or otherwise physically associated with a carbon nanotube to form a targeted protein-carbon nanotube complex.

  3. Computational Modelling in Cancer: Methods and Applications

    Directory of Open Access Journals (Sweden)

    Konstantina Kourou


    Full Text Available Computational modelling of diseases is an emerging field, proven valuable for the diagnosis, prognosis and treatment of the disease. Cancer is one of the diseases where computational modelling provides enormous advancements, allowing the medical professionals to perform in silico experiments and gain insights prior to any in vivo procedure. In this paper, we review the most recent computational models that have been proposed for cancer. Well known databases used for computational modelling experiments, as well as, the various markup language representations are discussed. In addition, recent state of the art research studies related to tumour growth and angiogenesis modelling are presented.

  4. Development of new therapeutic methods of lung cancer through team approach study

    Energy Technology Data Exchange (ETDEWEB)

    Park, Jong Ho; Zo, Jae Ill; Baek, Hee Jong; Jung, Jin Haeng; Lee, Jae Cheol; Ryoo, Baek Yeol; Kim, Mi Sook; Choi, Du Hwan; Park, Sun Young; Lee, Hae Young


    The aims of this study were to make the lung cancer clinics in Korea Cancer Center Hospital, and to establish new therapeutic methods of lung cancer for increasing the cure rate and survival rate of patients. Also another purpose of this study was to establish a common treatment method in our hospital. All patients who were operated in Korea Cancer Center Hospital from 1987 due to lung cancer were followed up and evaluated. And we have been studied the effect of postoperative adjuvant therapy in stage I, II, IIIA non-small cell lung cancer patients from 1989 with the phase three study form. Follow-up examinations were scheduled in these patients and interim analysis was made. Also we have been studied the effect of chemo-therapeutic agents in small cell lung cancer patients from 1997 with the phase two study form. We evaluated the results of this study. Some important results of this study were as follows. 1. The new therapeutic method (surgery + MVP chemotherapy) was superior to the standard therapeutic one in stage I Non-small cell lung cancer patients. So, we have to change the standard method of treatment in stage I NSCLC. 2. Also, this new therapeutic method made a good result in stage II NSCLC patients. And this result was reported in The Annals of Thoracic Surgery. 3. However, this new therapeutic method was not superior to the standard treatment method (surgery only) in stage IIIA NSCLC patients. So, we must develop new chemo-therapeutic agents in the future for advanced NSCLC patients. 4. In the results of the randomized phase II studies about small cell lung cancer, there was no difference in survival between Etoposide + Carboplatin + Ifosfamide + Cisplatin group and Etoposide + Carboplatin + Ifosfamide + Cisplatin + Tamoxifen group in both the limited and extended types of small cell lung cancer patients.

  5. Analysis of cytotoxic T cell epitopes in relation to cancer

    DEFF Research Database (Denmark)

    Stranzl, Thomas

    kill the infected cells. The focus of my PhD project has been on improving a method for CTL epitope pathway prediction, on analyzing the epitope density in the alternative cancer exome, and on a study investigating minor histocompatibility antigens (mHags) associated with leukemia. Part I......CTL methods, the experimental effort to identify 90% of new epitopes can be reduced by 15% and 40%, respectively. Part III reports the results of an analysis investigating how the alternatively spliced cancer exome differs from the exome of normal tissue in terms of containing predicted MHC class I binding...... epitopes. We show that peptides unique to cancer splice variants comprise significantly fewer predicted HLA class I epitopes than peptides unique to spliced transcripts in normal tissue. We furthermore find that hydrophilic amino acids are significantly enriched in the unique carcinoma sequences, which...

  6. Bayesian Methods for Statistical Analysis


    Puza, Borek


    Bayesian methods for statistical analysis is a book on statistical methods for analysing a wide variety of data. The book consists of 12 chapters, starting with basic concepts and covering numerous topics, including Bayesian estimation, decision theory, prediction, hypothesis testing, hierarchical models, Markov chain Monte Carlo methods, finite population inference, biased sampling and nonignorable nonresponse. The book contains many exercises, all with worked solutions, including complete c...

  7. Ultrasound Imaging Methods for Breast Cancer Detection

    NARCIS (Netherlands)

    Ozmen, N.


    The main focus of this thesis is on modeling acoustic wavefield propagation and implementing imaging algorithms for breast cancer detection using ultrasound. As a starting point, we use an integral equation formulation, which can be used to solve both the forward and inverse problems. This thesis c

  8. NIM: A Node Influence Based Method for Cancer Classification

    Directory of Open Access Journals (Sweden)

    Yiwen Wang


    Full Text Available The classification of different cancer types owns great significance in the medical field. However, the great majority of existing cancer classification methods are clinical-based and have relatively weak diagnostic ability. With the rapid development of gene expression technology, it is able to classify different kinds of cancers using DNA microarray. Our main idea is to confront the problem of cancer classification using gene expression data from a graph-based view. Based on a new node influence model we proposed, this paper presents a novel high accuracy method for cancer classification, which is composed of four parts: the first is to calculate the similarity matrix of all samples, the second is to compute the node influence of training samples, the third is to obtain the similarity between every test sample and each class using weighted sum of node influence and similarity matrix, and the last is to classify each test sample based on its similarity between every class. The data sets used in our experiments are breast cancer, central nervous system, colon tumor, prostate cancer, acute lymphoblastic leukemia, and lung cancer. experimental results showed that our node influence based method (NIM is more efficient and robust than the support vector machine, K-nearest neighbor, C4.5, naive Bayes, and CART.

  9. NIM: a node influence based method for cancer classification. (United States)

    Wang, Yiwen; Yao, Min; Yang, Jianhua


    The classification of different cancer types owns great significance in the medical field. However, the great majority of existing cancer classification methods are clinical-based and have relatively weak diagnostic ability. With the rapid development of gene expression technology, it is able to classify different kinds of cancers using DNA microarray. Our main idea is to confront the problem of cancer classification using gene expression data from a graph-based view. Based on a new node influence model we proposed, this paper presents a novel high accuracy method for cancer classification, which is composed of four parts: the first is to calculate the similarity matrix of all samples, the second is to compute the node influence of training samples, the third is to obtain the similarity between every test sample and each class using weighted sum of node influence and similarity matrix, and the last is to classify each test sample based on its similarity between every class. The data sets used in our experiments are breast cancer, central nervous system, colon tumor, prostate cancer, acute lymphoblastic leukemia, and lung cancer. experimental results showed that our node influence based method (NIM) is more efficient and robust than the support vector machine, K-nearest neighbor, C4.5, naive Bayes, and CART.

  10. Nested methylation-specific polymerase chain reaction cancer detection method (United States)

    Belinsky, Steven A.; Palmisano, William A.


    A molecular marker-based method for monitoring and detecting cancer in humans. Aberrant methylation of gene promoters is a marker for cancer risk in humans. A two-stage, or "nested" polymerase chain reaction method is disclosed for detecting methylated DNA sequences at sufficiently high levels of sensitivity to permit cancer screening in biological fluid samples, such as sputum, obtained non-invasively. The method is for detecting the aberrant methylation of the p16 gene, O 6-methylguanine-DNA methyltransferase gene, Death-associated protein kinase gene, RAS-associated family 1 gene, or other gene promoters. The method offers a potentially powerful approach to population-based screening for the detection of lung and other cancers.

  11. Analysis of Precision of Activation Analysis Method

    DEFF Research Database (Denmark)

    Heydorn, Kaj; Nørgaard, K.


    The precision of an activation-analysis method prescribes the estimation of the precision of a single analytical result. The adequacy of these estimates to account for the observed variation between duplicate results from the analysis of different samples and materials, is tested by the statistic T......, which is shown to be approximated by a χ2 distribution. Application of this test to the results of determinations of manganese in human serum by a method of established precision, led to the detection of airborne pollution of the serum during the sampling process. The subsequent improvement in sampling...... conditions was shown to give not only increased precision, but also improved accuracy of the results....

  12. Spatial methods in areal administrative data analysis

    Directory of Open Access Journals (Sweden)

    Haijun Ma


    Full Text Available Administrative data often arise as electronic copies of paid bills generated from insurance companies including the Medicare and Medicaid programs. Such data are widely seen and analyzed in the public health area, as in investigations of cancer control, health service accessibility, and spatial epidemiology. In areas like political science and education, administrative data are also important. Administrative data are sometimes more readily available as summaries over each administrative unit (county, zip code, etc. in a particular set determined by geopolitical boundaries, or what statisticians refer to as areal data. However, the spatial dependence often present in administrative data is often ignored by health services researchers. This can lead to problems in estimating the true underlying spatial surface, including inefficient use of data and biased conclusions. In this article, we review hierarchical statistical modeling and boundary analysis (wombling methods for areal-level spatial data that can be easily carried out using freely available statistical computing packages. We also propose a new edge-domain method designed to detect geographical boundaries corresponding to abrupt changes in the areal-level surface. We illustrate our methods using county-level breast cancer late detection data from the state of Minnesota.

  13. Advances in Gas Chromatographic Methods for the Identification of Biomarkers in Cancer

    Directory of Open Access Journals (Sweden)

    Konstantinos A. Kouremenos, Mikael Johansson, Philip J. Marriott


    Full Text Available Screening complex biological specimens such as exhaled air, tissue, blood and urine to identify biomarkers in different forms of cancer has become increasingly popular over the last decade, mainly due to new instruments and improved bioinformatics. However, despite some progress, the identification of biomarkers has shown to be a difficult task with few new biomarkers (excluding recent genetic markers being considered for introduction to clinical analysis. This review describes recent advances in gas chromatographic methods for the identification of biomarkers in the detection, diagnosis and treatment of cancer. It presents a general overview of cancer metabolism, the current biomarkers used for cancer diagnosis and treatment, a background to metabolic changes in tumors, an overview of current GC methods, and collectively presents the scope and outlook of GC methods in oncology.

  14. Comparative proteomics analysis of human gastric cancer

    Institute of Scientific and Technical Information of China (English)

    Wei Li; Jian-Fang Li; Ying Qu; Xue-Hua Chen; Jian-Min Qin; Qin-Long Gu; Min Yan; Zheng-Gang Zhu; Bing-Ya Liu


    AIM: To isolate and identify differentially expressed proteins between cancer and normal tissues of gastric cancer by two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS).METHODS: Soluble fraction proteins of gastric cancer tissues and paired normal tissues were separated by 2-DE.The differentially expressed proteins were selected and identified by MALDI-TOF-MS and database search.RESULTS: 2-DE profiles with high resolution and reproducibility were obtained.Twenty-three protein spots were excised from sliver staining gel and digested in gel by trypsin,in which fifteen protein spots were identified successfully.Among the identified proteins,there were ten over-expressed and five under-expressed proteins in stomach cancer tissues compared with normal tissues.CONCLUSION: In this study,the well-resolved,reproducible 2-DE patterns of human gastric cancer tissue and paired normal tissue were established and optimized and certain differentially-expressed proteins were identified.The combined use of 2-DE and MS provides an effective approach to screen for potential tumor markers.

  15. Review of "Cancer Nanotechnology: Methods and Protocols (Methods in Molecular Biology" by Stephen R. Grobmyer (Editor, Brij M. Moudgil (Editor

    Directory of Open Access Journals (Sweden)

    Steinmetz Nicole F


    Full Text Available Abstract Cancer remains one of the leading causes of death. Research and resulting technologies have contributed to rising numbers of cancer survivors. Cancer nanotechnology is a novel and burgeoning field with the promise to open the door for the development of improved cancer therapies and detection methods. Cancer nanotechnology has the potential to become clinical reality.

  16. Potential screening and early diagnosis method for cancer: Tongue diagnosis. (United States)

    Han, Shuwen; Yang, Xi; Qi, Quan; Pan, Yuefen; Chen, Yongchao; Shen, Junjun; Liao, Haihong; Ji, Zhaoning


    Tongue diagnosis, as a unique method of traditional Chinese medicine (TCM), was used to discriminate physiological functions and pathological conditions by observing the changes of the tongue and tongue coating. The aims of the present study were to explore a potential screening and early diagnosis method of cancer through evaluating the differences of the images of tongue and tongue coating and the microbiome on the tongue coating. The DS01-B tongue diagnostic information acquisition system was used to photograph and analyze the tongue and tongue coating. The next-generation sequencing technology was used to determine the V2-V4 hypervariable regions of 16S rDNA to investigate the microbiome on the tongue coating. Bioinformatics and statistical methods were used to analyze the microbial community structure and diversity. Comparing with the healthy people, the number of mirror-like tongue, thick tongue coating and the moisture of tongue were increased in cancers. The dominant color of the tongue in the healthy people was reddish while it was purple in the cancers. The relative abundance of Neisseria, Haemophilus, Fusobacterium and Porphyromonas in the healthy people were higher than that in the cancers. We also found 6 kinds of special microorganisms at species level in cancers. The study suggested that tongue diagnosis may provide potential screening and early diagnosis method for cancer.

  17. A new method for analyzing diagnostic delay in gynecological cancer

    DEFF Research Database (Denmark)

    Vandborg, Mai Partridge; Edwards, Kasper; Kragtrup, Jakob;


    OBJECTIVE: The aim of this article is to present a new methodology to illustrate, understand, and measure delay in health care. The method is inspired by process mapping tools as analytical framework and demonstrates its usefulness for studying diagnostic delay in gynecological cancer. MATERIALS...... AND METHODS: Six women with a diagnostic delay of 6 weeks or more before treatment of gynecological cancer at a specialized regional department (the Department of Gynecology and Obstetrics, Odense University Hospital, Denmark) were included in the study. Maps of existing processes were performed for each...... to responsibilities and was shown to recurrently influence and contribute to the delay in the diagnostic process. Some important contributors to diagnostic delay in gynecological cancer, such as lack of cancer suspicion, competing diseases, negative test results, inexpedient referral patterns, and referrals without...

  18. A New Method for Analyzing Diagnostic Delay in Gynecological Cancer

    DEFF Research Database (Denmark)

    Vandborg, Mai Partridge; Edwards, Kasper; Kragstrup, Jakob;


    OBJECTIVE: The aim of this article is to present a new methodology to illustrate, understand, and measure delay in health care. The method is inspired by process mapping tools as analytical framework and demonstrates its usefulness for studying diagnostic delay in gynecological cancer. MATERIALS...... AND METHODS: Six women with a diagnostic delay of 6 weeks or more before treatment of gynecological cancer at a specialized regional department (the Department of Gynecology and Obstetrics, Odense University Hospital, Denmark) were included in the study. Maps of existing processes were performed for each...... to responsibilities and was shown to recurrently influence and contribute to the delay in the diagnostic process. Some important contributors to diagnostic delay in gynecological cancer, such as lack of cancer suspicion, competing diseases, negative test results, inexpedient referral patterns, and referrals without...

  19. Selenium and lung cancer: a systematic review and meta analysis.

    Directory of Open Access Journals (Sweden)

    Heidi Fritz

    Full Text Available BACKGROUND: Selenium is a natural health product widely used in the treatment and prevention of lung cancers, but large chemoprevention trials have yielded conflicting results. We conducted a systematic review of selenium for lung cancers, and assessed potential interactions with conventional therapies. METHODS AND FINDINGS: Two independent reviewers searched six databases from inception to March 2009 for evidence pertaining to the safety and efficacy of selenium for lung cancers. Pubmed and EMBASE were searched to October 2009 for evidence on interactions with chemo- or radiation-therapy. In the efficacy analysis there were nine reports of five RCTs and two biomarker-based studies, 29 reports of 26 observational studies, and 41 preclinical studies. Fifteen human studies, one case report, and 36 preclinical studies were included in the interactions analysis. Based on available evidence, there appears to be a different chemopreventive effect dependent on baseline selenium status, such that selenium supplementation may reduce risk of lung cancers in populations with lower baseline selenium status (serum<106 ng/mL, but increase risk of lung cancers in those with higher selenium (≥ 121.6 ng/mL. Pooling data from two trials yielded no impact to odds of lung cancer, OR 0.93 (95% confidence interval 0.61-1.43; other cancers that were the primary endpoints of these trials, OR 1.51 (95%CI 0.70-3.24; and all-cause-death, OR 0.93 (95%CI 0.79-1.10. In the treatment of lung cancers, selenium may reduce cisplatin-induced nephrotoxicity and side effects associated with radiation therapy. CONCLUSIONS: Selenium may be effective for lung cancer prevention among individuals with lower selenium status, but at present should not be used as a general strategy for lung cancer prevention. Although promising, more evidence on the ability of selenium to reduce cisplatin and radiation therapy toxicity is required to ensure that therapeutic efficacy is maintained before


    Directory of Open Access Journals (Sweden)



    Full Text Available Audit sampling involves the application of audit procedures to less than 100% of items within an account balance or class of transactions. Our article aims to study audit sampling in audit of financial statements. As an audit technique largely used, in both its statistical and nonstatistical form, the method is very important for auditors. It should be applied correctly for a fair view of financial statements, to satisfy the needs of all financial users. In order to be applied correctly the method must be understood by all its users and mainly by auditors. Otherwise the risk of not applying it correctly would cause loose of reputation and discredit, litigations and even prison. Since there is not a unitary practice and methodology for applying the technique, the risk of incorrectly applying it is pretty high. The SWOT analysis is a technique used that shows the advantages, disadvantages, threats and opportunities. We applied SWOT analysis in studying the sampling method, from the perspective of three players: the audit company, the audited entity and users of financial statements. The study shows that by applying the sampling method the audit company and the audited entity both save time, effort and money. The disadvantages of the method are difficulty in applying and understanding its insight. Being largely used as an audit method and being a factor of a correct audit opinion, the sampling method’s advantages, disadvantages, threats and opportunities must be understood by auditors.

  1. Statistical methods for bioimpedance analysis

    Directory of Open Access Journals (Sweden)

    Christian Tronstad


    Full Text Available This paper gives a basic overview of relevant statistical methods for the analysis of bioimpedance measurements, with an aim to answer questions such as: How do I begin with planning an experiment? How many measurements do I need to take? How do I deal with large amounts of frequency sweep data? Which statistical test should I use, and how do I validate my results? Beginning with the hypothesis and the research design, the methodological framework for making inferences based on measurements and statistical analysis is explained. This is followed by a brief discussion on correlated measurements and data reduction before an overview is given of statistical methods for comparison of groups, factor analysis, association, regression and prediction, explained in the context of bioimpedance research. The last chapter is dedicated to the validation of a new method by different measures of performance. A flowchart is presented for selection of statistical method, and a table is given for an overview of the most important terms of performance when evaluating new measurement technology.

  2. Discrimination analysis of mass spectrometry proteomics for ovarian cancer detection

    Institute of Scientific and Technical Information of China (English)

    Yan-jun HONG; Xiao-dan WANG; David SHEN; Su ZENG


    Aim:A discrimination analysis has been explored for the probabilistic classifica-tion of healthy versus ovarian cancer serum samples using proteomics data from mass spectrometry (MS).Methods:The method employs data normalization,clustering,and a linear discriminant analysis on surface-enhanced laser desorp-tion ionization (SELDI) time-of-flight MS data.The probabilistic classification method computes the optimal linear discriminant using the complex human blood serum SELDI spectra.Cross-validation and training/testing data-split experi-ments are conducted to verify the optimal discriminant and demonstrate the accu-racy and robustness of the method.Results:The cluster discrimination method achieves excellent performance.The sensitivity,specificity,and positive predic-tive values are above 97% on ovarian cancer.The protein fraction peaks,which significantly contribute to the classification,can be available from the analysis process.Conclusion:The discrimination analysis helps the molecular identities of differentially expressed proteins and peptides between the healthy and ovarian patients.

  3. 染料法乳腺癌前哨淋巴结活检的多因素分析%Multivariate analysis of sentinel lymph node biopsy in breast cancer using blue dye methods

    Institute of Scientific and Technical Information of China (English)

    龚益平; 孙青海; 邵军; 程洪涛; 夏和顺; 熊斌


    Objective: Blue dye was one of the methods for sentinel lymph node biopsy in breast cancer, but the success rate was affected by multiple factors. This study was to determine the related factors contributing to the success of sentinel lymph node biopsy in breast cancer using blue dye method. Method:From Jan. 2007 to Aug.2008, sentinel lymph node biopsy was performed by periareolarly injecting 1% methylene blue in 141 breast cancer patients followed by axillary clearance. Pathological diagnosis was performed for all of the lymph nodes by conventional HE staining. Unconditional logistic regression was applied to make both univariate and multiva-riate analysis. Results:Sentinel lymph node was successfully detected in 126 patients. But the biopsy was failed in the 15 patients. The success rate was 89.4% and the false negative rate was 6.82%. Univariate analysis showed that success rate of biopsy was in association with patients' age, body mass index (BMI), tumor size, preoperative axillary node's status, pathological grade as well as ≥4 positive axillary lymph nodes involved. Multivariate analysis indicated that the patients'age (OR=4.587, P=0.024), BMI (OR=4.882, P=0.011) as well as 4 or more of the axillary nodes involved (OR=3.143, P=0.013) were independent predicting factors for the success of sentinel lymph node biopsy. Conclusions:Methylene blue dyeing is a reliable method for sentinel lymph node biopsy. The rate of success is associated with patients' age, BMI as well as the number of metastases in axillary lymph nodes.%目的:染料法是乳腺癌前哨淋巴结活检的方法之一,其成功率受多种因素影响.本研究旨在探讨影响染料法乳腺癌前哨淋巴结活检成功率的相关因素.方法:2007年1月-2008年8月乳腺癌患者141例,于乳晕周围注射1%亚甲蓝,实施前哨淋巴结活检,随后行腋窝淋巴结清扫,常规HE染色进行病理诊断.采用非条件logistic回归进行单因素和多因素分析.结果:126

  4. Obesity and Risk of Thyroid Cancer: Evidence from a Meta-Analysis of 21 Observational Studies (United States)

    Ma, Jie; Huang, Min; Wang, Li; Ye, Wei; Tong, Yan; Wang, Hanmin


    Background Several studies have evaluated the association between obesity and thyroid cancer risk. However, the results remain uncertain. In this study, we conducted a meta-analysis to assess the association between obesity and thyroid cancer risk. Material/Methods Published literature from PubMed, EMBASE, Springer Link, Ovid, Chinese Wanfang Data Knowledge Service Platform, Chinese National Knowledge Infrastructure (CNKI), and Chinese Biology Medicine (CBM) were retrieved before 10 August 2014. We included all studies that reported adjusted risk ratios (RRs), hazard ratios (HRs) or odds ratios (ORs), and 95% confidence intervals (CIs) of thyroid cancer risk. Results Thirty-two studies (n=12 620 676) were included in this meta-analysis. Obesity was associated with a significantly increased risk of thyroid cancer (adjusted RR=1.33; 95% CI, 1.24–1.42; I2=25%). In the subgroup analysis by study type, increased risk of thyroid cancer was found in cohort studies and case-control studies. In subgroup analysis by sex, both obese men and women were at significantly greater risk of thyroid cancer than non-obese subjects. When stratified by ethnicity, significantly elevated risk was observed in Caucasians and in Asians. In the age subgroup analysis, both young and old populations showed increased thyroid cancer risk. Subgroup analysis on smoking status showed that increased thyroid cancer risks were found in smokers and in non-smokers. In the histology subgroup analyses, increased risks of papillary thyroid cancer, follicular thyroid cancer, and anaplastic thyroid cancer were observed. However, obesity was associated with decreased risk of medullary thyroid cancer. Conclusions Our results indicate that obesity is associated with an increased thyroid cancer risk, except medullary thyroid cancer. PMID:25612155

  5. Analysis of breast cancer progression using principal component analysis and clustering

    Indian Academy of Sciences (India)

    G Alexe; G S Dalgin; S Ganesan; C DeLisi; G Bhanot


    We develop a new technique to analyse microarray data which uses a combination of principal components analysis and consensus ensemble -clustering to find robust clusters and gene markers in the data. We apply our method to a public microarray breast cancer dataset which has expression levels of genes in normal samples as well as in three pathological stages of disease; namely, atypical ductal hyperplasia or ADH, ductal carcinoma in situ or DCIS and invasive ductal carcinoma or IDC. Our method averages over clustering techniques and data perturbation to find stable, robust clusters and gene markers. We identify the clusters and their pathways with distinct subtypes of breast cancer (Luminal, Basal and Her2+). We confirm that the cancer phenotype develops early (in early hyperplasia or ADH stage) and find from our analysis that each subtype progresses from ADH to DCIS to IDC along its own specific pathway, as if each was a distinct disease.

  6. Differential Regulatory Analysis Based on Coexpression Network in Cancer Research

    Directory of Open Access Journals (Sweden)

    Junyi Li


    Full Text Available With rapid development of high-throughput techniques and accumulation of big transcriptomic data, plenty of computational methods and algorithms such as differential analysis and network analysis have been proposed to explore genome-wide gene expression characteristics. These efforts are aiming to transform underlying genomic information into valuable knowledges in biological and medical research fields. Recently, tremendous integrative research methods are dedicated to interpret the development and progress of neoplastic diseases, whereas differential regulatory analysis (DRA based on gene coexpression network (GCN increasingly plays a robust complement to regular differential expression analysis in revealing regulatory functions of cancer related genes such as evading growth suppressors and resisting cell death. Differential regulatory analysis based on GCN is prospective and shows its essential role in discovering the system properties of carcinogenesis features. Here we briefly review the paradigm of differential regulatory analysis based on GCN. We also focus on the applications of differential regulatory analysis based on GCN in cancer research and point out that DRA is necessary and extraordinary to reveal underlying molecular mechanism in large-scale carcinogenesis studies.

  7. cDNA macroarray for analysis of gene expression profiles in prostate cancer

    Institute of Scientific and Technical Information of China (English)


    Background Early diagnosis and timely treatment are important for improving therapeutic efficiency of prostate cancer. DNA array is a new bio-technology for disease diagnosis. This study was conducted to diagnose prostate cancer with cDNA macroarray and analysis gene expression profiles of some selective genes in prostate cancer.Methods Total RNA was isolated from patients with prostate cancer and from normal people, and poly(A) RNA was further purified. Then it was analyzed for differentially expressed genes in prostate cancer and normal prostate by cDNA macroarray system.Results There were different expressions in the nine prostate-associated specific genes in prostate cancer as compared with normal prostate, in which, 7 were significantly upregulated and 2 were down-regulated.Conclusion As a diagnostic approach at molecular level, the cDNA macroarray is an effectively diagnostic method for prostate cancer.

  8. DNA adducts and cancer risk in prospective studies: a pooled analysis and a meta-analysis

    DEFF Research Database (Denmark)

    Veglia, Fabrizio; Loft, Steffen; Matullo, Giuseppe;


    Bulky DNA adducts are biomarkers of exposure to aromatic compounds and of the ability of the individual to metabolically activate carcinogens and to repair DNA damage. Their ability to predict cancer onset is uncertain. We have performed a pooled analysis of three prospective studies on cancer risk...... in which bulky DNA adducts have been measured in blood samples collected from healthy subjects (N = 1947; average follow-up 51-137 months). In addition, we have performed a meta-analysis by identifying all articles on the same subject published up to the end of 2006, including case-control studies....... In the pooled analysis, a weakly statistically significant increase in the risk of lung cancer was apparent (14% per unit standard deviation change in adduct levels, 95% confidence interval 1-28%; using the weighted mean difference method, 0.15 SD, units higher adducts in cases than in controls...

  9. Investigation of the molecular relationship between breast cancer and obesity by candidate gene prioritization methods

    Directory of Open Access Journals (Sweden)

    Saba Garshasbi


    Full Text Available Background: Cancer and obesity are two major public health concerns. More than 12 million cases of cancer are reported annually. Many reports confirmed obesity as a risk factor for cancer. The molecular relationship between obesity and breast cancer has not been clear yet. The purpose of this study was to investigate priorities of effective genes in the molecular relationship between obesity and breast cancer. Methods: In this study, computer simulation method was used for prioritizing the genes that involved in the molecular links between obesity and breast cancer in laboratory of systems biology and bioinformatics (LBB, Tehran University, Tehran, Iran, from March to July 2014. In this study, ENDEAVOUR software was used for prioritizing the genes and integrating multiple data sources was used for data analysis. Training genes were selected from effective genes in obesity and/or breast cancer. Two groups of candidate genes were selected. The first group was included the existential genes in 5 common region chromosomes (between obesity and breast cancer and the second group was included the results of genes microarray data analysis of research Creighton, et al (In 2012 on patients with breast cancer. The microarray data were analyzed with GER2 software (R online software on GEO website. Finally, both training and candidate genes were entered in ENDEAVOUR software package. Results: The candidate genes were prioritized to four style and five genes in ten of the first priorities were repeated twice. In other word, the outcome of prioritizing of 72 genes (Product of microarray data analysis and genes of 5 common chromosome regions (Between obesity and breast cancer showed, 5 genes (TNFRSF10B, F2, IGFALS, NTRK3 and HSP90B1 were the priorities in the molecular connection between obesity and breast cancer. Conclusion: There are some common genes between breast cancer and obesity. So, molecular relationship is confirmed. In this study the possible effect

  10. Nonlinear programming analysis and methods

    CERN Document Server

    Avriel, Mordecai


    Comprehensive and complete, this overview provides a single-volume treatment of key algorithms and theories. The author provides clear explanations of all theoretical aspects, with rigorous proof of most results. The two-part treatment begins with the derivation of optimality conditions and discussions of convex programming, duality, generalized convexity, and analysis of selected nonlinear programs. The second part concerns techniques for numerical solutions and unconstrained optimization methods, and it presents commonly used algorithms for constrained nonlinear optimization problems. This g

  11. Analysis methods for airborne radioactivity


    Ala-Heikkilä, Jarmo J


    High-resolution gamma-ray spectrometry is an analysis method well suitable for monitoring airborne radioactivity. Many of the natural radionuclides and a majority of anthropogenic nuclides are prominent gamma-ray emitters. With gamma-ray spectrometry different radionuclides are readily observed at minute concentrations that are far from health hazards. The gamma-ray spectrometric analyses applied in air monitoring programmes can be divided into particulate measurements and gas measurements. I...

  12. Gait analysis methods in rehabilitation

    Directory of Open Access Journals (Sweden)

    Baker Richard


    Full Text Available Abstract Introduction Brand's four reasons for clinical tests and his analysis of the characteristics of valid biomechanical tests for use in orthopaedics are taken as a basis for determining what methodologies are required for gait analysis in a clinical rehabilitation context. Measurement methods in clinical gait analysis The state of the art of optical systems capable of measuring the positions of retro-reflective markers placed on the skin is sufficiently advanced that they are probably no longer a significant source of error in clinical gait analysis. Determining the anthropometry of the subject and compensating for soft tissue movement in relation to the under-lying bones are now the principal problems. Techniques for using functional tests to determine joint centres and axes of rotation are starting to be used successfully. Probably the last great challenge for optical systems is in using computational techniques to compensate for soft tissue measurements. In the long term future it is possible that direct imaging of bones and joints in three dimensions (using MRI or fluoroscopy may replace marker based systems. Methods for interpreting gait analysis data There is still not an accepted general theory of why we walk the way we do. In the absence of this, many explanations of walking address the mechanisms by which specific movements are achieved by particular muscles. A whole new methodology is developing to determine the functions of individual muscles. This needs further development and validation. A particular requirement is for subject specific models incorporating 3-dimensional imaging data of the musculo-skeletal anatomy with kinematic and kinetic data. Methods for understanding the effects of intervention Clinical gait analysis is extremely limited if it does not allow clinicians to choose between alternative possible interventions or to predict outcomes. This can be achieved either by rigorously planned clinical trials or using

  13. Green Tea Consumption and Stomach Cancer Risk: A Meta-Analysis


    Kang, Hyunseok; Rha, Sun Young; Oh, Kyung Won; Nam, Chung Mo


    OBJECTIVES Green tea has been suggested to have a chemopreventive effect against various cancers including stomach cancer. The aim of this study is to elucidate the relationship between green tea consumption and stomach cancer risk by meta-analysis. METHODS Eighteen observational studies were identified using MEDLINE, THE COCHRANE LIBRARY, RISS, and a manual search. Summary relative risks/odds ratios (RR/ORs) for the highest versus non/lowest green tea consumption levels were calculated on th...

  14. Metabolic Syndrome Is Associated with Increased Breast Cancer Risk: A Systematic Review with Meta-Analysis


    Ruchi Bhandari; Kelley, George A; Hartley, Tara A.; Rockett, Ian R. H.


    Background. Although individual metabolic risk factors are reported to be associated with breast cancer risk, controversy surrounds risk of breast cancer from metabolic syndrome (MS). We report the first systematic review and meta-analysis of the association between MS and breast cancer risk in all adult females. Methods. Studies were retrieved by searching four electronic reference databases [PubMed, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Web of Science, and ProQu...

  15. Epidemiology of lung cancer and approaches for its prediction:a systematic review and analysis

    Institute of Scientific and Technical Information of China (English)

    Ashutosh Kumar Dubey; Umesh Gupta; Sonal Jain


    Background: Owing to the use of tobacco and the consumption of alcohol and adulterated food, worldwide cancer incidence is increasing at an alarming and frightening rate. Since the last decade of the twentieth century, lung can-cer has been the most common cancer type. This study aimed to determine the global status of lung cancer and to evaluate the use of computational methods in the early detection of lung cancer. Methods: We used lung cancer data from the United Kingdom (UK), the United States (US), India, and Egypt. For statistical analysis, we used incidence and mortality as well as survival rates to better understand the critical state of lung cancer. Results: In the UK and the US, we found a significant decrease in lung cancer mortalities in the period of 1990–2014, whereas, in India and Egypt, such a decrease was not much promising. Additionally, we observed that, in the UK and the US, the survival rates of women with lung cancer were higher than those of men. We observed that the data min-ing and evolutionary algorithms were efcient in lung cancer detection. Conclusions: Our findings provide an inclusive understanding of the incidences, mortalities, and survival rates of lung cancer in the UK, the US, India, and Egypt. The combined use of data mining and evolutionary algorithm can be efcient in lung cancer detection.

  16. Cancer Nursing Education: Literature Review and Documentary Analysis. (United States)

    Langton, Helen; Blunden, Gillian; Hek, Gill

    The knowledge and skills needed by cancer nurses and the content and strategies of England's existing cancer nursing education programs were examined. The study included a comprehensive literature review and an analysis of course documents from selected English National Board-approved post-qualifying cancer nursing and palliative care courses…

  17. Association of OPN rs11730582 polymorphism with cancer risk: a meta-analysis

    Directory of Open Access Journals (Sweden)

    He LL


    Full Text Available Lanlan He,1,* Yong Wang2,* 1Emergency Department, Zhenjiang First People’s Hospital, Zhenjiang, People’s Republic of China; 2Department of Interventional Radiology and Vascular Surgery, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, People’s Republic of China *Both authors contributed equally to this work Purpose: Several molecular epidemiological studies have investigated the association between OPN rs11730582 C>T polymorphism and cancer risk, but the results are inconsistent. Hence, a meta-analysis was conducted to determine the association of this polymorphism with cancer risk. Materials and methods: The related articles were searched in PubMed, Embase, and Chinese National Knowledge Infrastructure databases. Pooled odds ratios and 95% confidence intervals were calculated to evaluate the strength of the associations. A random-effects model or fixed-effects model was employed depending on the heterogeneity. Results: A total of ten case-control studies involving 2,749 cancer cases and 3,398 controls were included in the meta-analysis. In overall analysis, OPN rs11730582 C>T polymorphism was not associated with cancer risk. In a stratified analysis by cancer type, no significant association was found between OPN rs11730582 C>T polymorphism and the risk of glioma, gastric cancer, and other cancers. Conclusion: This meta-analysis suggests that OPN rs11730582 C>T polymorphism is not associated with cancer susceptibility. Keywords: osteopontin, polymorphism, cancer, risk 

  18. Segmentation and Analysis of Cancer Cells in Blood Samples

    Directory of Open Access Journals (Sweden)

    Arjun Nelikanti


    Full Text Available Blood cancer is an umbrella term for cancers that affect the blood, bone marrow and lymphatic system. Acute Lymphoblastic Leukemia (ALL is one of the kinds of blood cancer which can be affected at any age in the humans. The analysis of peripheral blood samples is an important test in the procedures for the diagnosis of leukemia. In this paper the blood sample images are used and implementing a clustering algorithm for detection of the cancer cells. This paper also implements morphological operations and feature extraction techniques using MATLAB for the analysis of cancer cells in the images.

  19. [Sentinel lymph node biopsy in endometrial cancer - methods]. (United States)

    Yordanov, G; Gorchev, S; Tomov, N; Hinkova


    Endometrial canceris the most common gynaecological malignancy after brest cancer. The lymph node status is with great prognostic value and it is important for postoperative treatment and survival. That is why it is looking for methods giving information for the lymph node status and not increasing postoperative complications.


    Directory of Open Access Journals (Sweden)

    Ivan Valeriu


    Full Text Available Keeping a company in the top performing players in the relevant market depends not only on its ability to develop continually, sustainably and balanced, to the standards set by the customer and competition, but also on the ability to protect its strategic information and to know in advance the strategic information of the competition. In addition, given that economic markets, regardless of their profile, enable interconnection not only among domestic companies, but also between domestic companies and foreign companies, the issue of economic competition moves from the national economies to the field of interest of regional and international economic organizations. The stakes for each economic player is to keep ahead of the competition and to be always prepared to face market challenges. Therefore, it needs to know as early as possible, how to react to others’ strategy in terms of research, production and sales. If a competitor is planning to produce more and cheaper, then it must be prepared to counteract quickly this movement. Competitive intelligence helps to evaluate the capabilities of competitors in the market, legally and ethically, and to develop response strategies. One of the main goals of the competitive intelligence is to acknowledge the role of early warning and prevention of surprises that could have a major impact on the market share, reputation, turnover and profitability in the medium and long term of a company. This paper presents some aspects of competitive intelligence, mainly in terms of information analysis and intelligence generation. Presentation is theoretical and addresses a structured method of information analysis - scenarios method – in a version that combines several types of analysis in order to reveal some interconnecting aspects of the factors governing the activity of a company.

  1. Cancer (United States)

    ... cancer Non-Hodgkin lymphoma Ovarian cancer Pancreatic cancer Testicular cancer Thyroid cancer Uterine cancer Symptoms Symptoms of cancer ... tumor Obesity Pancreatic cancer Prostate cancer Stomach cancer Testicular cancer Throat or larynx cancer Thyroid cancer Patient Instructions ...


    Directory of Open Access Journals (Sweden)

    Katarina Bevizova


    Full Text Available Malignant cancers of urinary bladder are the second most common malignancy of the urinary tract and the fourth most common malignancy in general, especially in men. The aim of this study was a retrospective analysis of selected markers (p53, Ki-67 and E-cadherin of urinary bladder cancers from the Department of Urology in Bratislava, Slovak Republic between years 2007 and 2009. We analysed 244 patients (202 males, 42 females with diagnosed bladder cancer via cystoscopy and subsequent transurethral resection. Patients’ age varied from 36 to 98 years. Obtained samples were fixed by 10% buffered formalin for 24 to 48 h. Subsequently, they were dehydrated in ascending ethanol series and embedded in paraffin. The parafin sections of 5 µm were prepared by microtome and they were stained by haematoxylin and eosin. The antibodies against to p53, Ki-67 and E-cadherin were used in immunohistochemical analysis. Statistical evaluation was performed via SPSS using non-parametric Kruskal-Wallis test and p values<0.05 were considered statistically significant. No significant differences in the expression of selected markers were found between genders. Expression of p53 and Ki-67, in G1 and G2 of low grade tumours was lower in comparison to their expression in G3 tumors. Expression of E-cadherin was the opposite in this case. The expression of p53 and Ki-67 positively correlated with tumor’s depth of invasion, while the expression of E-cadherin significantly decreased. In case of T4 tumors, the expression of all markers exhibited consistently high values. When analysing tumor multiplicity, the expression of p53 and Ki-67 significantly decreased, while the expression of E-cadherin significantly increased. Based on the obtained results it can be concluded that the analysis of p53, Ki-67 and E-cadherin expression is essential for diagnostics and prognostics of bladder cancer and should be routinely used in daily practise together with

  3. Nanotechnology Method Comparison for Early Detection of Cancer

    Directory of Open Access Journals (Sweden)

    Wamakshi Bhati


    Full Text Available Since 1999, cancer has been the leading cause of death under the age of 85 years and the eradication of this disease has been the long sought-after goal of scientists and physicians. Cancer is a disease in which abnormal cells divide uncontrollably. These abnormal cells have the ability to invade and destroy normal body cells, which is life threatening. One of the most important factors in effective cancer treatment is the detection of cancerous tumour cells in an early stage. Nanotechnology brings new hope to the arena of cancer detection research, owing to nanoparticles’ unique physical and chemical properties, giving them the potential to be used in the detection and monitoring of cancer. One such approach is quantum dots based detection which is rapid, easy and economical enabling quick point-of-care screening of cancer markers. QDs have got unique properties which make them ideal for detecting tumours. On the other hand, Gold nanoparticles have been in the bio-imaging spotlight due to their special optical properties. Au-NPs with strong surface-plasmon-enhanced absorption and scattering have allowed them to emerge as powerful imaging labels and contrast agents. This paper includes the comparative study of both the methods. Compared with quantum dots, the gold-nanoparticles are more than 200 times brighter on a particle-to-particle basis, although they are about 60 times larger by volume. Thus, Gold nanoparticles in suspension, offers advantages compared with quantum dots in that the gold appears to be non-toxic and the particles produce a brighter, sharper signal.

  4. Breast cancer tumor classification using LASSO method selection approach

    Energy Technology Data Exchange (ETDEWEB)

    Celaya P, J. M.; Ortiz M, J. A.; Martinez B, M. R.; Solis S, L. O.; Castaneda M, R.; Garza V, I.; Martinez F, M.; Ortiz R, J. M., E-mail: [Universidad Autonoma de Zacatecas, Av. Ramon Lopez Velarde 801, Col. Centro, 98000 Zacatecas, Zac. (Mexico)


    Breast cancer is one of the leading causes of deaths worldwide among women. Early tumor detection is key in reducing breast cancer deaths and screening mammography is the widest available method for early detection. Mammography is the most common and effective breast cancer screening test. However, the rate of positive findings is very low, making the radiologic interpretation monotonous and biased toward errors. In an attempt to alleviate radiological workload, this work presents a computer-aided diagnosis (CAD x) method aimed to automatically classify tumor lesions into malign or benign as a means to a second opinion. The CAD x methos, extracts image features, and classifies the screening mammogram abnormality into one of two categories: subject at risk of having malignant tumor (malign), and healthy subject (benign). In this study, 143 abnormal segmentation s (57 malign and 86 benign) from the Breast Cancer Digital Repository (BCD R) public database were used to train and evaluate the CAD x system. Percentile-rank (p-rank) was used to standardize the data. Using the LASSO feature selection methodology, the model achieved a Leave-one-out-cross-validation area under the receiver operating characteristic curve (Auc) of 0.950. The proposed method has the potential to rank abnormal lesions with high probability of malignant findings aiding in the detection of potential malign cases as a second opinion to the radiologist. (Author)

  5. CRCDA--Comprehensive resources for cancer NGS data analysis. (United States)

    Thangam, Manonanthini; Gopal, Ramesh Kumar


    Next generation sequencing (NGS) innovations put a compelling landmark in life science and changed the direction of research in clinical oncology with its productivity to diagnose and treat cancer. The aim of our portal comprehensive resources for cancer NGS data analysis (CRCDA) is to provide a collection of different NGS tools and pipelines under diverse classes with cancer pathways and databases and furthermore, literature information from PubMed. The literature data was constrained to 18 most common cancer types such as breast cancer, colon cancer and other cancers that exhibit in worldwide population. NGS-cancer tools for the convenience have been categorized into cancer genomics, cancer transcriptomics, cancer epigenomics, quality control and visualization. Pipelines for variant detection, quality control and data analysis were listed to provide out-of-the box solution for NGS data analysis, which may help researchers to overcome challenges in selecting and configuring individual tools for analysing exome, whole genome and transcriptome data. An extensive search page was developed that can be queried by using (i) type of data [literature, gene data and sequence read archive (SRA) data] and (ii) type of cancer (selected based on global incidence and accessibility of data). For each category of analysis, variety of tools are available and the biggest challenge is in searching and using the right tool for the right application. The objective of the work is collecting tools in each category available at various places and arranging the tools and other data in a simple and user-friendly manner for biologists and oncologists to find information easier. To the best of our knowledge, we have collected and presented a comprehensive package of most of the resources available in cancer for NGS data analysis. Given these factors, we believe that this website will be an useful resource to the NGS research community working on cancer. Database URL:

  6. Pattern Analysis and Decision Support for Cancer through Clinico-Genomic Profiles (United States)

    Exarchos, Themis P.; Giannakeas, Nikolaos; Goletsis, Yorgos; Papaloukas, Costas; Fotiadis, Dimitrios I.

    Advances in genome technology are playing a growing role in medicine and healthcare. With the development of new technologies and opportunities for large-scale analysis of the genome, genomic data have a clear impact on medicine. Cancer prognostics and therapeutics are among the first major test cases for genomic medicine, given that all types of cancer are related with genomic instability. In this paper we present a novel system for pattern analysis and decision support in cancer. The system integrates clinical data from electronic health records and genomic data. Pattern analysis and data mining methods are applied to these integrated data and the discovered knowledge is used for cancer decision support. Through this integration, conclusions can be drawn for early diagnosis, staging and cancer treatment.

  7. Two cytological methods for screening for cervical cancer

    DEFF Research Database (Denmark)

    Kirschner, B.; Simonsen, K.; Junge, J.


    INTRODUCTION: Denmark has had an organized screening programme for cervical cancer since the 1960s. In spite of this, almost 150 Danish women die from the disease each year. There are currently two different methods for preparation of cervical samples: conventional Papanicolaou smear and liquid......-based cytology. MATERIALS AND METHODS: In 2002, the Department of Pathology, Hvidovre Hospital changed over from the conventional Papanicolaou smear screening method to SurePath liquid-based cytology. This article is based on a retrospective comparison on data from the population screening programme for cervical...... cancer in the Municipality of Copenhagen. RESULTS: The number of tests with the diagnosis of "normal cells" decreased 1% after the conversion to liquid-based cytology, whilst the number of tests with "atypical cells" and "cells suspicious for malignancy" increased by 64.3% and 41.2% respectively...

  8. Current Status of Methods to Assess Cancer Drug Resistance

    Directory of Open Access Journals (Sweden)

    Theodor H. Lippert, Hans-Jörg Ruoff, Manfred Volm


    Full Text Available Drug resistance is the main cause of the failure of chemotherapy of malignant tumors, resistance being either preexisting (intrinsic resistance or induced by the drugs (acquired resistance. At present, resistance is usually diagnosed during treatment after a long period of drug administration.In the present paper, methods for a rapid assessment of drug resistance are described. Three main classes of test procedures can be found in the literature, i.e. fresh tumor cell culture tests, cancer biomarker tests and positron emission tomography (PET tests. The methods are based on the evaluation of molecular processes, i.e. metabolic activities of cancer cells. Drug resistance can be diagnosed before treatment in-vitro with fresh tumor cell culture tests, and after a short time of treatment in-vivo with PET tests. Cancer biomarker tests, for which great potential has been predicted, are largely still in the development stage. Individual resistance surveillance with tests delivering rapid results signifies progress in cancer therapy management, by providing the possibility to avoid drug therapies that are ineffective and only harmful.

  9. Meta-analysis of intraperitoneal chemotherapy for gastric cancer

    Institute of Scientific and Technical Information of China (English)

    Da-Zhi Xu; You-Qing Zhan; Xiao-Wei Sun; Su-Mei Cao; Qi-Rong Geng


    AIM: To assess the efficacy and safety of intraperitoneal chemotherapy in patients undergoing curative resection for gastric cancer through literature review. METHODS: Medline (PubMed) (1980-2003/1), Embase (1980-2003/1), Cancerlit Database (1983-2003/1) and Chinese Biomedicine Database (1990-2003/1) were searched. Language was restricted to Chinese and English. The statistical analysis was performed by RevMan4.2 software provided by the Cochrane Collaboration. The results were expressed with odds ratio for the categorical variables. RESULTS: Eleven trials involving 1 161 cases were included. The pooled odds ratio was 0.51, with a 95% confidence interval (0.40-0.65). Intraperitoneal chemotherapy may benefit the patients after curative resection for locally advanced gastric cancer, and the combination of intraperitoneal chemotherapy with hyperthermia or activated carbon particles may provide more benefits to patients due to the enhanced antitumor activity of drugs. Sensitivity analysis and fail-safe number suggested that the result was comparatively reliable. However, of 11 trials, only 3 studies were of high quality. CONCLUSION: Intraperitoneal chemotherapy after curative resection for locally advanced gastric cancer may be beneficial to patients. Continuous multicenter, randomized, double blind, rigorously designed trials should be conducted to draw definitive conclusions.

  10. Which is better for gastric cancer patients, perioperative or adjuvant chemotherapy: a meta-analysis



    Background The preferred chemotherapy method for gastric cancer continues to be matter of debate. We performed a meta-analysis to comparing prognosis and safety between perioperative chemotherapy and adjuvant chemotherapy to identify the better chemotherapy option for gastric cancer. Methods We searched the PubMed, EMBASE, Cochrane Library, and Ovid databases for eligible studies until February 2016. The main endpoints were prognostic value (hazard ratio [HR] for overall survival [OS] and 1-,...

  11. Treatment of skin and subcutaneous cancer diseases by hyperthermic methods

    Directory of Open Access Journals (Sweden)

    Zviad Kovziridze


    Full Text Available Purpose: The present work pursues perfection of highly efficient anticancer, principally new methodology and technology. It deals with the comparative study of anticancer activity of controlled local hyperthermia in animals and determination-de- velopment of optimal regimes and schemes. Furthermore, it also presents the work on new clinical device of high anticancer effect. Methods: Authors used controlled local hyperthermia for this study. In our experiments, we used 3 to 3.5 months-old non-pedigree (nonlinear white mice (mass: 18-30 gram. After mice selection for the experiments, animals were placed in vivarium, in quarantine regime for 10 to 4 days. Individual protocols were drawn for each animal. Similar feeding and handling regimes were created for all animals. Transplantable malignant cancer strain, Erlich adenocarcinoma, was used. Results: Experiments on animals were successful. There are positive conclusions of pathological-anatomy laboratory “PathGeo”: Form # IV -200- 6A, for the examination # 3119-12 and # 15/02 and macro-morphological and micro-morphological description of the study # 15272-13. On the basis of the results of morphological study, it was proved that liver and lungs (the main target bodies were intact, and secondary cancer injuries were not fixed. After three sessions of hyperthermia treatment, the decrease in sizes of cancer formations and necrosis of diseased sections were visualized, while massive necrosis was observed after seven sessions. In all cases, necrosis and ulceration of diseased places were observed, which refers to transition of cancer into phase of healing. After eight-ten sessions, necrosis of cancer and ulceration were observed, which refers to irreversibility of the process and efficiency of the applied method of hyperthermia. Conclusion: Anticancer effect of hyperthermia conditioned by temperature fields was proved, which was expressed in inhibition of cancer growth, resorption and increase of

  12. Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps. (United States)

    Kuperstein, I; Bonnet, E; Nguyen, H-A; Cohen, D; Viara, E; Grieco, L; Fourquet, S; Calzone, L; Russo, C; Kondratova, M; Dutreix, M; Barillot, E; Zinovyev, A


    Cancerogenesis is driven by mutations leading to aberrant functioning of a complex network of molecular interactions and simultaneously affecting multiple cellular functions. Therefore, the successful application of bioinformatics and systems biology methods for analysis of high-throughput data in cancer research heavily depends on availability of global and detailed reconstructions of signalling networks amenable for computational analysis. We present here the Atlas of Cancer Signalling Network (ACSN), an interactive and comprehensive map of molecular mechanisms implicated in cancer. The resource includes tools for map navigation, visualization and analysis of molecular data in the context of signalling network maps. Constructing and updating ACSN involves careful manual curation of molecular biology literature and participation of experts in the corresponding fields. The cancer-oriented content of ACSN is completely original and covers major mechanisms involved in cancer progression, including DNA repair, cell survival, apoptosis, cell cycle, EMT and cell motility. Cell signalling mechanisms are depicted in detail, together creating a seamless 'geographic-like' map of molecular interactions frequently deregulated in cancer. The map is browsable using NaviCell web interface using the Google Maps engine and semantic zooming principle. The associated web-blog provides a forum for commenting and curating the ACSN content. ACSN allows uploading heterogeneous omics data from users on top of the maps for visualization and performing functional analyses. We suggest several scenarios for ACSN application in cancer research, particularly for visualizing high-throughput data, starting from small interfering RNA-based screening results or mutation frequencies to innovative ways of exploring transcriptomes and phosphoproteomes. Integration and analysis of these data in the context of ACSN may help interpret their biological significance and formulate mechanistic hypotheses

  13. Investigation of Common Symptoms of Cancer and Reliability Analysis

    Institute of Scientific and Technical Information of China (English)


    Objective: To identify cancer distribution and treatment requirements, a questionnaire on cancer patients was conducted. It was our objective to validate a series of symptoms commonly used in traditional Chinese medicine (TCM). Methods: The M. D. Anderson Symptom Assessment Inventory (MDASI) was used with 10 more TCM items added. Questions regarding TCM application requested in cancer care were also asked. A multi-center, cross-sectional study was conducted in 340 patients from 4 hospitals in Beijing and Dalian. SPSS and Excel software were adopted for statistical analysis. The questionnaire was self-evaluated with the Cronbach's alpha score. Results: The most common symptoms were fatigue 89.4%, sleep disturbance 74.4%, dry mouth 72.9%, poor appetite 72.9%, and difficulty remembering 71.2%. These symptoms affected work (89.8%), mood (82.6%),and activity (76.8%), resulting in poor quality of life. Eighty percent of the patients wanted to regulate the body with TCM. Almost 100% of the patients were interested in acquiring knowledge regarding the integrated traditional Chinese medicine (TCM) and Western medicine (WM) in the treatment and rehabilitation of cancer. Cronbach's alpha score indicated that there was acceptable internal consistency within both the MDASI and TCM items, 0.86 for MDASI, 0.78 for TCM, and 0.90 for MDASI-TCM (23 items). Conclusions: Fatigue, sleep disturbance, dry mouth, poor appetite, and difficulty remembering are the most common symptoms in cancer patients. These greatly affect the quality of life for these patients. Patients expressed a strong desire for TCM holistic regulation. The MDASI and its TCM-adapted model could be a critical tool for the quantitative study of TCM symptoms.

  14. Alternative Methods to Treat Nausea and Vomiting from Cancer Chemotherapy

    Directory of Open Access Journals (Sweden)

    Mohammad Ali Sheikhi


    Full Text Available Chemotherapy Induced Nausea and Vomiting (CINV is among the most intensive side effects and critical concerns for patients with cancer. Most of these patients experience nausea and vomiting after chemotherapy. Sometimes, this is so annoying that it may prevent them from continuing the therapy. With the recent advances, a variety of therapeutic methods are innovated and applied to control CINV. Among them, the main methods include medicinal therapy, relaxation, and herbal therapy. Yet, using dexamethasone together with massage therapy and ginger is identified as the most effective method.

  15. Gene selection for microarray cancer classification using a new evolutionary method employing artificial intelligence concepts. (United States)

    Dashtban, M; Balafar, Mohammadali


    Gene selection is a demanding task for microarray data analysis. The diverse complexity of different cancers makes this issue still challenging. In this study, a novel evolutionary method based on genetic algorithms and artificial intelligence is proposed to identify predictive genes for cancer classification. A filter method was first applied to reduce the dimensionality of feature space followed by employing an integer-coded genetic algorithm with dynamic-length genotype, intelligent parameter settings, and modified operators. The algorithmic behaviors including convergence trends, mutation and crossover rate changes, and running time were studied, conceptually discussed, and shown to be coherent with literature findings. Two well-known filter methods, Laplacian and Fisher score, were examined considering similarities, the quality of selected genes, and their influences on the evolutionary approach. Several statistical tests concerning choice of classifier, choice of dataset, and choice of filter method were performed, and they revealed some significant differences between the performance of different classifiers and filter methods over datasets. The proposed method was benchmarked upon five popular high-dimensional cancer datasets; for each, top explored genes were reported. Comparing the experimental results with several state-of-the-art methods revealed that the proposed method outperforms previous methods in DLBCL dataset.

  16. Rectal cancer surgery: volume-outcome analysis.

    LENUS (Irish Health Repository)

    Nugent, Emmeline


    There is strong evidence supporting the importance of the volume-outcome relationship with respect to lung and pancreatic cancers. This relationship for rectal cancer surgery however remains unclear. We review the currently available literature to assess the evidence base for volume outcome in relation to rectal cancer surgery.

  17. Establishment and application of a multiplex genetic mutation-detection method of lung cancer based on MassARRAY platform

    Institute of Scientific and Technical Information of China (English)

    Hong-Xia Tian; Xu-Chao Zhang; Zhen Wang; Jian-Guang Chen; Shi-Liang Chen; Wei-Bang Guo; Yi-Long Wu


    Objective:This study aims to establish a method for highly parallel multiplexed detection of genetic mutations in Chinese lung cancer samples through Agena iPLEX chemistry and matrix-assisted laser desorption ionization time-of-flight analysis on MassARRAY mass spectrometry platform. Methods:We reviewed the related literature and data on lung cancer treatments. We also identified 99 mutation hot spots in 13 target genes closely related to the pathogenesis, drug resistance, and metastasis of lung cancer. A total of 297 primers, composed of 99 paired forward and reverse amplification primers and 99 matched extension primers, were designed using Assay Design software. The detection method was established by analyzing eight cell lines and six lung cancer specimens. The proposed method was then validated through comparisons by using a LungCartaTM kit. The sensitivity and specificity of the proposed method were evaluated by directly sequencingEGFR andKRAS genes in 100 lung cancer cases. Results:The proposed method was able to detect multiplex genetic mutations in lung cancer cell lines. This finding was consistent with the observations on previously reported mutations. The proposed method can also detect such mutations in clinical lung cancer specimens. This result was consistent with the observations with LungCartaTM kit. However, anFGFR2 mutation was detected only through the proposed method. The measured sensitivity and specificity were 100% and 96.3%, respectively. Conclusions:The proposed MassARRAY technology-based multiplex method can detect genetic mutations in Chinese lung cancer patients. Therefore, the proposed method can be applied to detect mutations in other cancer tissues.

  18. Saliva analysis combining membrane protein purification with surface-enhanced Raman spectroscopy for nasopharyngeal cancer detection (United States)

    Feng, Shangyuan; Lin, Duo; Lin, Juqiang; Huang, Zufang; Chen, Guannan; Li, Yongzeng; Huang, Shaohua; Zhao, Jianhua; Chen, Rong; Zeng, Haishan


    A method for saliva analysis combining membrane protein purification with silver nanoparticle-based surface-enhanced Raman spectroscopy (SERS) for non-invasive nasopharyngeal cancer detection was present in this paper. In this method, cellulose acetate membrane was used to obtain purified whole proteins from human saliva while removing other native saliva constituents and exogenous substances. The purified proteins were mixed with silver nanoparticle for SERS analysis. A diagnostic accuracy of 90.2% can be achieved by principal components analysis combined with linear discriminate analysis, for saliva samples obtained from patients with nasopharyngeal cancer (n = 62) and healthy volunteers (n = 30). This exploratory study demonstrated the potential for developing non-invasive, rapid saliva SERS analysis for nasopharyngeal cancer detection.

  19. Survey and Analysis of Awareness of Lung Cancer Prevention and Control in a LDCT Lung Cancer Screening Project in Tianjin Dagang Oilfield of China

    Directory of Open Access Journals (Sweden)

    Guanhua REN


    Full Text Available Background and objective It has been proven that increase of the awareness level of lung cancer prevention and control could enhance participation of lung cancer screening of lung cancer high risk group. The aim of this study is to investigate the awareness level of lung cancer prevention and control and the effect of individual characteristics on lung cancer awareness, and to provide evidence for comprehensive lung cancer prevention in high risk areas of lung cancer. Methods Staffs of Tianjin Dagang Oil Field who participate low dose CT (LDCT lung cancer screening by cluster sampling or according to voluntary principle were surveyed, data of lung cancer awareness were collected by questionnaire. Results A total of 1,633 valid questionnaires were collected. The average age of respondents was 60.08±6.58. Most participants were males (82.2% while female only accounted for 17.8%. The proportions of awareness about lung cancer in China, risk factors, screening methods and the knowledge of health examination were 64.5%, 77.1%, 43.7%, 49.6% respectively. Result of multiple logistic regression analysis showed that education level, smoking (pack-year, age, prior tuberculosis were the influencing factors of lung cancer awareness with adjusted Ors for education and age level as of 0.567 (95%CI: 0.439-0.733 and 1.373 (95%CI: 1.084-1.739 respectively. 80.3% of the participants can accept health examination once a year, while the ability to pay the medical expenses was not high. The influencing factors of health examination willingness were gender, age, income, the knowledge of lung cancer. Conclusion Education level and smoking affect the awareness of lung cancer prevention and control, health education for lung cancer should be conducted especially in population with low education level. Comprehensive lung cancer control in high risk areas should combined lung cancer screening, tobacco control and health education.

  20. An approach for the identification of targets specific to bone metastasis using cancer genes interactome and gene ontology analysis.

    Directory of Open Access Journals (Sweden)

    Shikha Vashisht

    Full Text Available Metastasis is one of the most enigmatic aspects of cancer pathogenesis and is a major cause of cancer-associated mortality. Secondary bone cancer (SBC is a complex disease caused by metastasis of tumor cells from their primary site and is characterized by intricate interplay of molecular interactions. Identification of targets for multifactorial diseases such as SBC, the most frequent complication of breast and prostate cancers, is a challenge. Towards achieving our aim of identification of targets specific to SBC, we constructed a 'Cancer Genes Network', a representative protein interactome of cancer genes. Using graph theoretical methods, we obtained a set of key genes that are relevant for generic mechanisms of cancers and have a role in biological essentiality. We also compiled a curated dataset of 391 SBC genes from published literature which serves as a basis of ontological correlates of secondary bone cancer. Building on these results, we implement a strategy based on generic cancer genes, SBC genes and gene ontology enrichment method, to obtain a set of targets that are specific to bone metastasis. Through this study, we present an approach for probing one of the major complications in cancers, namely, metastasis. The results on genes that play generic roles in cancer phenotype, obtained by network analysis of 'Cancer Genes Network', have broader implications in understanding the role of molecular regulators in mechanisms of cancers. Specifically, our study provides a set of potential targets that are of ontological and regulatory relevance to secondary bone cancer.

  1. Growth Analysis of Cancer Biology Research, 2000-2011

    Directory of Open Access Journals (Sweden)



    Full Text Available Methods and Material: The PubMed database was used for retrieving data on 'cancer biology.' Articles were downloaded from the years 2000 to 2011. The articles were classified chronologically and transferred to a spreadsheet application for analysis of the data as per the objectives of the study. Statistical Method: To investigate the nature of growth of articles via exponential, linear, and logistics tests. Result: The year wise analysis of the growth of articles output shows that for the years 2000 to 2005 and later there is a sudden increase in output, during the years 2006 to 2007 and 2008 to 2011. The high productivity of articles during these years may be due to their significance in cancer biology literature, having received prominence in research. Conclusion: There is an obvious need for better compilations of statistics on numbers of publications in the years from 2000 to 2011 on various disciplines on a worldwide scale, for informed critical assessments of the amount of new knowledge contributed by these publications, and for enhancements and refinements of present Scientometric techniques (citation and publication counts, so that valid measures of knowledge growth may be obtained. Only then will Scientometrics be able to provide accurate, useful descriptions and predictions of knowledge growth.

  2. Consortium analysis of 7 candidate SNPs for ovarian cancer

    DEFF Research Database (Denmark)

    Ramus, S.J.; Vierkant, R.A.; Johnatty, S.E.


    The Ovarian Cancer Association Consortium selected 7 candidate single nucleotide polymorphisms (SNPs), for which there is evidence from previous studies of an association with variation in ovarian cancer or breast cancer risks. The SNPs selected for analysis were F31I (rs2273535) in AURKA, N372H...... for SNPs identified from relatively large initial studies shows the importance of replicating associations by a consortium approach Udgivelsesdato: 2008/7/15...

  3. Rapid coal proximate analysis by thermogravimetric method

    Energy Technology Data Exchange (ETDEWEB)

    Mao Jianxiong; Yang Dezhong; Zhao Baozhong


    A rapid coal proximate analysis by thermogravimetric analysis (TGA) can be used as an alternative method for the standard proximate analysis. This paper presents a program set up to rapidly perform coal proximate analysis by using a thermal analyzer and TGA module. A comparison between coal proximate analyses by standard method (GB) and TGA is also given. It shows that most data from TGA fall within the tolerance limit of standard method.

  4. p53 codon 72 polymorphism and liver cancer susceptibility: A meta-analysis of epidemiologic studies

    Institute of Scientific and Technical Information of China (English)

    Xi Chen; Fei Liu; Bo Li; Yong-Gang Wei; Lv-Nan Yan; Tian-Fu Wen


    AIM: To evaluate the association between p53 codon 72 polymorphism and liver cancer risk by means of meta-analysis.METHODS: Two investigators independently searched the Medline, Embase and Chinese Biomedicine databas-es. Summary odds ratios and 95% CI for p53 codon 72 polymorphism and liver cancer were calculated in .xed-effects model (Mantel-Haenszel method) and random-effects model (DerSimonian and Laird method) when appropriate.RESULTS: This meta-analysis included 1115 liver can-cer cases and 1778 controls. The combined results based on all studies showed that there was a statisti-cally signi.cant link between Pro/Pro genotype and liver cancer, but not between Arg/Arg or Pro/Arg genotype and liver cancer. When stratifying for race, similar re-sults were obtained, i.e. patients with liver cancer had a signi.cantly higher frequency of Pro/Pro genotype than non-cancer patients among Asians. After stratifying the various studies by control source, gender, family history of liver cancer and chronic hepatitis virus infection, we found that (1) patients among hospital-based studies had a significantly higher frequency of Pro/Pro and a signi.cantly lower frequency of Arg/Arg genotype than individuals without cancer; (2) female patients with liver cancer had a significantly lower frequency of Arg/Arg and a higher frequency of Pro/Arg+Pro/Pro genotypes than female individuals without cancer; (3) subgroup analyses for family history of liver cancer did not re-veal any signi.cant association between p53 codon 72 polymorphism and liver cancer development; and (4) patients with negative hepatitis virus infection had a sig-ni.cantly higher frequency of Pro/Pro and a signi.cantly lower frequency of Arg/Arg genotype than individuals without cancer.CONCLUSION: This meta-analysis suggests that the p53 codon 72 polymorphism may be associated with liver cancer among Asians.

  5. Prostate Cancer Patients’ Refusal of Cancer-Directed Surgery: A Statewide Analysis

    Directory of Open Access Journals (Sweden)

    K. M. Islam


    Full Text Available Introduction. Prostate cancer is the most common cancer among men in USA. The surgical outcomes of prostate cancer remain inconsistent. Barriers such as socioeconomic factors may play a role in patients’ decision of refusing recommended cancer-directed surgery. Methods. The Nebraska Cancer Registry data was used to calculate the proportion of prostate cancer patients recommended the cancer-directed surgery and the surgery refusal rate. Multivariate logistic regression was applied to analyze the socioeconomic indicators that were related to the refusal of surgery. Results. From 1995 to 2012, 14,876 prostate cancer patients were recommended to undergo the cancer-directed surgery in Nebraska, and 576 of them refused the surgery. The overall refusal rate of surgery was 3.9% over the 18 years. Patients with early-stage prostate cancer were more likely to refuse the surgery. Patients who were Black, single, or covered by Medicaid/Medicare had increased odds of refusing the surgery. Conclusion. Socioeconomic factors were related to the refusal of recommended surgical treatment for prostate cancer. Such barriers should be addressed to improve the utilization of surgical treatment and patients’ well-being.

  6. Application of a Computational Method for the Early Diagnosis of Prostate Cancer Using Proteomic Pattern Recognition

    Directory of Open Access Journals (Sweden)

    Elzenir Montes,


    Full Text Available This paper presents a method based on the recognition of proteomic patterns for the early diagnosis of prostate cancer, using computational techniques, applied in the database of SELDI-TOF proteomic patterns. The method is based on classifying the individual as to the portability stage of prostate cancer. To do so, the Independent Component Analysis (ICA technique is used to extract the characteristics, after which are utilized the algorithm of Maximum Relevance and Minimum Redundancy to reduce the computational cost, and finally the Support Vector Machine to obtain the classification. The best result of the method was obtained with a vector of 27 characteristics, achieving accuracy, specificity and sensitivity, respectively of 89.21%, 83.68% and 95.08%.

  7. Analysis of intratumor heterogeneity unravels lung cancer evolution


    Bruin, Elza C de; McGranahan, Nicholas; Swanton, Charles


    Lung cancer is a disease with dismal outcome. We recently reported a detailed intratumor heterogeneity analysis in 7 non-small cell lung cancer samples, revealing spatially separated driver events as well as the temporal dynamics of mutational processes and demonstrating an important role for APOBEC-mediated heterogeneity later in disease evolution.

  8. Diagnostic model of saliva protein finger print analysis of patients with gastric cancer

    Institute of Scientific and Technical Information of China (English)

    Zheng-Zhi Wu; Ji-Guo Wang; Xiao-Li Zhang


    AIM: To explore the method for early diagnosis of gastric cancer by screening the expression spectrum of saliva protein in gastric cancer patients using mass spectrometry for proteomics. METHODS: Proportional peptide mass fingerprints were obtained by analysis based on proteomics matrixassisted laser desorption ionization time-of-flight/mass spectrometry. A diagnosis model was established using weak cation exchange magnetic beads to test saliva specimens from gastric cancer patients and healthy subjects. RESULTS: Significant differences were observed in the mass to charge ratio (m/z) peaks of four proteins (1472.78 Da, 2936.49 Da, 6556.81 Da and 7081.17 Da) between gastric cancer patients and healthy subjects. CONCLUSION: The finger print mass spectrum of saliva protein in patients with gastric cancer can be established using gastric cancer proteomics. A diagnostic model for distinguishing protein expression mass spectra of gastric cancer from non-gastriccancer saliva can be established according to the different expression of proteins 1472.78 Da, 2936.49 Da, 6556.81 Da and 7081.17 Da. The method for early diagnosis of gastric cancer is of certain value for screening special biological markers.

  9. Comparative Proteomic Analysis of Anti-Cancer Mechanism by Periplocin Treatment in Lung Cancer Cells

    Directory of Open Access Journals (Sweden)

    Zejun Lu


    Full Text Available Background: Periplocin is used for treatment of rheumatoid arthritis, reinforcement of bones and tendons, palpitations or shortness of breath and lower extremity edema in traditional medicine. Our previous findings suggested that periplocin could inhibit the growth of lung cancer both in vitro and in vivo. But the biological processes and molecular pathways by which periplocin induces these beneficial effects remain largely undefined. Methods: To explore the molecular mechanisms of periplocin involved in anti-cancer activity, in the present study the protein profile changes of human lung cancer cell lines A549 in response to periplocin treatment were investigated using the proteomics approaches (2-DE combined with MS/MS. Western blot was employed to verify the changed proteins. Interactions between changed proteins were analyzed by STRING. Results: 29 down-regulated protein species named GTP-binding nuclear protein Ran (RAN, Rho GDP-dissociation inhibitor 1 (ARHGDIA, eukaryotic translation initiation factor 5A-1 (EIF5A and Profilin-1(PFN1, and 10 up-regulated protein species named Heat shock cognate 71 kDa protein (HSPA8,10 kDa heat shock protein (HSPE1, and Cofilin-1(CFL-1 were identified. Among them, GTP-binding nuclear protein Ran (RAN and Rho GDP-dissociation inhibitor 1 (ARHGDIA were the most significantly changed (over tenfold. The proteasome subunit beta type-6 (PSMB6, ATP synthase ecto-α-subunit (ATP5A1, Aldehyde dehydrogenase 1 (ALDH1 and EIF5A were verified by immunoblot assays to be dramatically down-regulated. By STRING bioinformatics analysis revealing interactions and signaling networks it became apparent that the proteins changed they are primarily involved in transcription and proteolysis. Conclusion: Periplocin inhibited growth of lung cancer by down-regulating proteins, such as ATP5A1, EIF5A, ALDH1 and PSMB6. These findings may improve our understanding of the molecular mechanisms underlying the anti-cancer effects of

  10. Odds ratio analysis in women with endometrial cancer

    Directory of Open Access Journals (Sweden)

    Katarzyna Plagens-Rotman


    Full Text Available Introduction : Despite the progress in diagnosis and treatment of malignant tumours, the effects of treatment are insufficient. Reduction of the risk of cervical, ovarian, and endometrial cancer is possible by introducing preventative actions. Aim of the study: The aim of the thesis is the analysis of selected risk factors that may affect the increase or decrease in the odds ratio of developing endometrial cancer. Material and methods: The study was conducted among patients of the Gynaecology and Obstetrics Hospital of Poznań University of Medical Sciences in the years 2011-2013. The research included a total of 548 female respondents aged between 40 and 84 years. Women responded to questions assessing elements of lifestyle such as consumption of alcohol, smoking, and eating certain groups of foods. Results: The respondents consuming fruits and vegetables several times a week have a reduced risk of odds ratio and the OR is 0.85; 95% CI: 0.18-4.09, compared to the women who rarely consume vegetables and fruits. Consumption of whole-wheat bread several times a week reduces the risk of developing the cancer, OR = 0.59; 95% CI: 0.14-2.47, compared to women not consuming wholegrain bread at all. Respondents who consumed red meat, such as veal, pork, and lamb in the amount of 101-200 g per day have an increased risk of developing the disease: OR = 2.16; 95% CI: 1.09-4.28, compared to women not consuming red meat at all. Conclusions : A diet rich in fruit and vegetables, onions, garlic, whole grains, and beans should be introduced in order to reduce the risk of endometrial cancer. The consumption of red meat and white pasta should be reduced or even eliminated.

  11. Molecular analysis of precursor lesions in familial pancreatic cancer.

    Directory of Open Access Journals (Sweden)

    Tatjana Crnogorac-Jurcevic

    Full Text Available BACKGROUND: With less than a 5% survival rate pancreatic adenocarcinoma (PDAC is almost uniformly lethal. In order to make a significant impact on survival of patients with this malignancy, it is necessary to diagnose the disease early, when curative surgery is still possible. Detailed knowledge of the natural history of the disease and molecular events leading to its progression is therefore critical. METHODS AND FINDINGS: We have analysed the precursor lesions, PanINs, from prophylactic pancreatectomy specimens of patients from four different kindreds with high risk of familial pancreatic cancer who were treated for histologically proven PanIN-2/3. Thus, the material was procured before pancreatic cancer has developed, rather than from PanINs in a tissue field that already contains cancer. Genome-wide transcriptional profiling using such unique specimens was performed. Bulk frozen sections displaying the most extensive but not microdissected PanIN-2/3 lesions were used in order to obtain the holistic view of both the precursor lesions and their microenvironment. A panel of 76 commonly dysregulated genes that underlie neoplastic progression from normal pancreas to PanINs and PDAC were identified. In addition to shared genes some differences between the PanINs of individual families as well as between the PanINs and PDACs were also seen. This was particularly pronounced in the stromal and immune responses. CONCLUSIONS: Our comprehensive analysis of precursor lesions without the invasive component provides the definitive molecular proof that PanIN lesions beget cancer from a molecular standpoint. We demonstrate the need for accumulation of transcriptomic changes during the progression of PanIN to PDAC, both in the epithelium and in the surrounding stroma. An identified 76-gene signature of PDAC progression presents a rich candidate pool for the development of early diagnostic and/or surveillance markers as well as potential novel preventive

  12. Prognostic Analysis System and Methods of Operation (United States)

    MacKey, Ryan M. E. (Inventor); Sneddon, Robert (Inventor)


    A prognostic analysis system and methods of operating the system are provided. In particular, a prognostic analysis system for the analysis of physical system health applicable to mechanical, electrical, chemical and optical systems and methods of operating the system are described herein.

  13. Music as a method of coping with cancer: A qualitative study among cancer patients in Sweden. (United States)

    Ahmadi, Fereshteh


    Background: This study investigated patients' understanding of the role of music in coping and in influencing their well-being. Methods: A qualitative study was conducted based on semi-structured interviews with 17 cancer patients. Participants were chosen from a group of patients who had listened to or played music as a means of coping with their illness. Results: The study shows the importance of considering the roles that different kinds of music play in coping with cancer. The music of nature, healing music, religious music and cheerful music each have different benefits for patients. Conclusions: A patient's situation and his or her individual characteristics determine the types of music that can act as a useful or harmful coping strategy. Therefore, it is essential to investigate the types of individual characteristics that can make listening to different kinds of music a helpful or harmful coping method.

  14. Pan-cancer analysis of ROS1 genomic aberrations


    Wang, Yidan; 王奕丹


    The ROS proto-oncogene 1 (ROS1) encodes the ROS1 receptor kinase. ROS1 rearrangements are known to be oncogenic in glioblastoma, non–small-cell lung carcinoma (NSCLC) and cholangiocarcinoma. The clinical relevance of ROS1 genomic aberrations in other human cancers is largely unexamined. Here, we performed a pan-cancer analysis of ROS1 genomic aberrations across 20 cancer sites by interrogating the whole-exome sequencing data of the Cancer Genome Atlas (TCGA) via the cBioportal (www.cbioportal...

  15. Epidemiology and Survival Analysis of Jordanian Female Breast Cancer Patients Diagnosed from 1997 to 2002

    Directory of Open Access Journals (Sweden)

    Ghazi Sharkas


    Full Text Available Background: Breast cancer is the most common cancer among Jordanian women, yet survival data are scarce. This study aims to assess the observed five-year survival rate of breast cancer in Jordan from 1997 to 2002 and to determine factors that may influence survival. Methods: Data were obtained from the Jordan Cancer Registry (JCR, which is a population-based registry. From 1997-2002, 2121 patients diagnosed with breast cancer were registered in JCR. Relevant data were collected from JCR files, hospital medical records and histopathology reports. Patient's status, whether alive or dead, wasascertained from the Department of Civil Status using patients’ national numbers (ID. Statistical analysis was carried out using SPSS (version 10. Survival probabilities by age, morphology, grade, stage and other relevant variables were obtained with the Kaplan Meier method. Results: The overall five-year survival for breast cancer in Jordan, regardless of the stage or grade was 64.2%, meanwhile it was 58% in the group aged less than 30 years. The best survival was in the age group 40-49 years (69.3%. The survival for adenocarcinoma was 57.4% and for medullary carcinoma, it was 82%. The survival rate approximated 73.8% for well-differentiated, 55.6% for anaplastic, and 58% for poorly differentiated cancers. The five-year survival rate was 82.7% for stage I, 72.2% for stage II, 58.7% for stage III, and 34.6% for stage IV cancers.Conclusion: According to univariate analysis, stage, grade, age and laterality of breast cancer significantly influenced cancer survival. Cox regression analysis revealed that stage, grade and age factors correlated with prognosis, while laterality showed no significant effect on survival. Results demonstrated that overall survival was relatively poor. We hypothesized that this was due to low levels of awareness and lack of screening programs.

  16. Automatic diagnosis for prostate cancer using run-length matrix method (United States)

    Sun, Xiaoyan; Chuang, Shao-Hui; Li, Jiang; McKenzie, Frederic


    Prostate cancer is the most common type of cancer and the second leading cause of cancer death among men in US1. Quantitative assessment of prostate histology provides potential automatic classification of prostate lesions and prediction of response to therapy. Traditionally, prostate cancer diagnosis is made by the analysis of prostate-specific antigen (PSA) levels and histopathological images of biopsy samples under microscopes. In this application, we utilize a texture analysis method based on the run-length matrix for identifying tissue abnormalities in prostate histology. A tissue sample was collected from a radical prostatectomy, H&E fixed, and assessed by a pathologist as normal tissue or prostatic carcinoma (PCa). The sample was then subsequently digitized at 50X magnification. We divided the digitized image into sub-regions of 20 X 20 pixels and classified each sub-region as normal or PCa by a texture analysis method. In the texture analysis, we computed texture features for each of the sub-regions based on the Gray-level Run-length Matrix(GL-RLM). Those features include LGRE, HGRE and RPC from the run-length matrix, mean and standard deviation of the pixel intensity. We utilized a feature selection algorithm to select a set of effective features and used a multi-layer perceptron (MLP) classifier to distinguish normal from PCa. In total, the whole histological image was divided into 42 PCa and 6280 normal regions. Three-fold cross validation results show that the proposed method achieves an average classification accuracy of 89.5% with a sensitivity and specificity of 90.48% and 89.49%, respectively.

  17. Breast cancer in Iran: need for greater women awareness of warning signs and effective screening methods

    Directory of Open Access Journals (Sweden)

    Montazeri Ali


    Full Text Available Abstract Background Breast cancer remains an important public health problem. This study aimed to investigate about female knowledge of breast cancer and self-reported practice of breast self-examination in Iran. Methods This was a population-based survey carried out in Tehran, Iran. Data were collected via a structured questionnaire containing 15 questions on demographic status, history of personal and family breast problems, subjective knowledge about breast cancer covering its symptoms, the screening methods and practice of breast self-examination (BSE. A trained female nurse interviewed each respondent. Analysis included descriptive statistics and the Chi-squared test where necessary. Results A total of 1402 women were interviewed. The mean age of respondents was 43.4 (SD = 14.4 years; most were married (85%, and without any personal (94% and family history (90% of breast problems. It was found that 64% of the respondents were familiar with breast cancer and 61% (n = 851 believed that 'the disease is relatively common among women in Iran'. Most women (44% perceived a painless mass as a breast cancer symptom. Overall, 61% of the respondents stated that they knew about breast cancer screening programs and most indicated that electronic media (television 34% and radio 14% were their source of information. Only 17% of women said that 'they were conducting regular breast self-examination'. The main reason for women not doing breast self-examination was due to the fact that they did not know how to do it (64%. The findings indicated that performing breast self-examination is significantly related to: age, marital status, education, knowledge of breast cancer and knowledge about breast cancer screening programs (p Conclusion This descriptive study provides useful information that could be utilized by both researchers and those involved in public health programmes. The findings indicated that the women awareness of breast cancer warning signs

  18. Convergence analysis of combinations of different methods

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Y. [Clarkson Univ., Potsdam, NY (United States)


    This paper provides a convergence analysis for combinations of different numerical methods for solving systems of differential equations. The author proves that combinations of two convergent linear multistep methods or Runge-Kutta methods produce a new convergent method of which the order is equal to the smaller order of the two original methods.

  19. Probabilistic methods in combinatorial analysis

    CERN Document Server

    Sachkov, Vladimir N


    This 1997 work explores the role of probabilistic methods for solving combinatorial problems. These methods not only provide the means of efficiently using such notions as characteristic and generating functions, the moment method and so on but also let us use the powerful technique of limit theorems. The basic objects under investigation are nonnegative matrices, partitions and mappings of finite sets, with special emphasis on permutations and graphs, and equivalence classes specified on sequences of finite length consisting of elements of partially ordered sets; these specify the probabilist

  20. Chemometric techniques on the analysis of Raman spectra of serum blood samples of breast cancer patients (United States)

    Rocha-Osornio, L. N.; Pichardo-Molina, J. L.; Barbosa-Garcia, O.; Frausto-Reyes, C.; Araujo-Andrade, C.; Huerta-Franco, R.; Gutiérrez-Juárez, G.


    Raman spectroscopy and Multivariate methods were used to study serum blood samples of control and breast cancer patients. Blood samples were obtained from 11 patients and 12 controls from the central region of Mexico. Our results show that principal component analysis is able to discriminate serum sample of breast cancer patients from those of control group, also the loading vectors of PCA plotted as a function of Raman shift shown which bands permitted to make the maximum discrimination between both groups of samples.

  1. Cruciferous vegetables consumption and the risk of ovarian cancer: a meta-analysis of observational studies


    Han, Bo; Li, Xuepeng; Yu, Tao


    Background To quantify the effect of cruciferous vegetable consumption on the incidence of ovarian cancer by meta-analyzing the existing observational studies and provides quantitative and high-level evidence. Methods A detailed literature search of Medline and EMBASE for all relevant papers published. A meta-analysis was conducted for the association between cruciferous vegetable consumption and risk of ovarian cancer. Results A total of 4,306 cases in 375,562 controls in 11 independent stud...

  2. Neoadjuvant chemotherapy for advanced gastric cancer:A meta-analysis

    Institute of Scientific and Technical Information of China (English)


    AIM:To study the value of neoadjuvant chemotherapy (NAC) for advanced gastric cancer by performing a meta-analysis of the published studies.METHODS:All published controlled trials of NAC for advanced gastric cancer vs no therapy before surgery were searched.Studies that included patients with metastases at enrollment were excluded.Databases included Cochrane Library of Clinical Comparative Trials,MEDLINE,Embase,and American Society of Clinical Oncology meeting abstracts from 1978 to 2010.The censor date was...

  3. Applying critical analysis - main methods

    Directory of Open Access Journals (Sweden)

    Miguel Araujo Alonso


    Full Text Available What is the usefulness of critical appraisal of literature? Critical analysis is a fundamental condition for the correct interpretation of any study that is subject to review. In epidemiology, in order to learn how to read a publication, we must be able to analyze it critically. Critical analysis allows us to check whether a study fulfills certain previously established methodological inclusion and exclusion criteria. This is frequently used in conducting systematic reviews although eligibility criteria are generally limited to the study design. Critical analysis of literature and be done implicitly while reading an article, as in reading for personal interest, or can be conducted in a structured manner, using explicit and previously established criteria. The latter is done when formally reviewing a topic.

  4. A novel method, digital genome scanning detects KRAS gene amplification in gastric cancers: involvement of overexpressed wild-type KRAS in downstream signaling and cancer cell growth

    Directory of Open Access Journals (Sweden)

    Yanagihara Kazuyoshi


    Full Text Available Abstract Background Gastric cancer is the third most common malignancy affecting the general population worldwide. Aberrant activation of KRAS is a key factor in the development of many types of tumor, however, oncogenic mutations of KRAS are infrequent in gastric cancer. We have developed a novel quantitative method of analysis of DNA copy number, termed digital genome scanning (DGS, which is based on the enumeration of short restriction fragments, and does not involve PCR or hybridization. In the current study, we used DGS to survey copy-number alterations in gastric cancer cells. Methods DGS of gastric cancer cell lines was performed using the sequences of 5000 to 15000 restriction fragments. We screened 20 gastric cancer cell lines and 86 primary gastric tumors for KRAS amplification by quantitative PCR, and investigated KRAS amplification at the DNA, mRNA and protein levels by mutational analysis, real-time PCR, immunoblot analysis, GTP-RAS pull-down assay and immunohistochemical analysis. The effect of KRAS knock-down on the activation of p44/42 MAP kinase and AKT and on cell growth were examined by immunoblot and colorimetric assay, respectively. Results DGS analysis of the HSC45 gastric cancer cell line revealed the amplification of a 500-kb region on chromosome 12p12.1, which contains the KRAS gene locus. Amplification of the KRAS locus was detected in 15% (3/20 of gastric cancer cell lines (8–18-fold amplification and 4.7% (4/86 of primary gastric tumors (8–50-fold amplification. KRAS mutations were identified in two of the three cell lines in which KRAS was amplified, but were not detected in any of the primary tumors. Overexpression of KRAS protein correlated directly with increased KRAS copy number. The level of GTP-bound KRAS was elevated following serum stimulation in cells with amplified wild-type KRAS, but not in cells with amplified mutant KRAS. Knock-down of KRAS in gastric cancer cells that carried amplified wild

  5. Trial Sequential Methods for Meta-Analysis (United States)

    Kulinskaya, Elena; Wood, John


    Statistical methods for sequential meta-analysis have applications also for the design of new trials. Existing methods are based on group sequential methods developed for single trials and start with the calculation of a required information size. This works satisfactorily within the framework of fixed effects meta-analysis, but conceptual…

  6. Esophageal cancer prediction based on qualitative features using adaptive fuzzy reasoning method

    Directory of Open Access Journals (Sweden)

    Raed I. Hamed


    Full Text Available Esophageal cancer is one of the most common cancers world-wide and also the most common cause of cancer death. In this paper, we present an adaptive fuzzy reasoning algorithm for rule-based systems using fuzzy Petri nets (FPNs, where the fuzzy production rules are represented by FPN. We developed an adaptive fuzzy Petri net (AFPN reasoning algorithm as a prognostic system to predict the outcome for esophageal cancer based on the serum concentrations of C-reactive protein and albumin as a set of input variables. The system can perform fuzzy reasoning automatically to evaluate the degree of truth of the proposition representing the risk degree value with a weight value to be optimally tuned based on the observed data. In addition, the implementation process for esophageal cancer prediction is fuzzily deducted by the AFPN algorithm. Performance of the composite model is evaluated through a set of experiments. Simulations and experimental results demonstrate the effectiveness and performance of the proposed algorithms. A comparison of the predictive performance of AFPN models with other methods and the analysis of the curve showed the same results with an intuitive behavior of AFPN models.

  7. Pathway analysis of bladder cancer genome-wide association study identifies novel pathways involved in bladder cancer development (United States)

    Chen, Meng; Rothman, Nathaniel; Ye, Yuanqing; Gu, Jian; Scheet, Paul A.; Huang, Maosheng; Chang, David W.; Dinney, Colin P.; Silverman, Debra T.; Figueroa, Jonine D.; Chanock, Stephen J.; Wu, Xifeng


    Genome-wide association studies (GWAS) are designed to identify individual regions associated with cancer risk, but only explain a small fraction of the inherited variability. Alternative approach analyzing genetic variants within biological pathways has been proposed to discover networks of susceptibility genes with additional effects. The gene set enrichment analysis (GSEA) may complement and expand traditional GWAS analysis to identify novel genes and pathways associated with bladder cancer risk. We selected three GSEA methods: Gen-Gen, Aligator, and the SNP Ratio Test to evaluate cellular signaling pathways involved in bladder cancer susceptibility in a Texas GWAS population. The candidate genetic polymorphisms from the significant pathway selected by GSEA were validated in an independent NCI GWAS. We identified 18 novel pathways (P < 0.05) significantly associated with bladder cancer risk. Five of the most promising pathways (P ≤ 0.001 in any of the three GSEA methods) among the 18 pathways included two cell cycle pathways and neural cell adhesion molecule (NCAM), platelet-derived growth factor (PDGF), and unfolded protein response pathways. We validated the candidate polymorphisms in the NCI GWAS and found variants of RAPGEF1, SKP1, HERPUD1, CACNB2, CACNA1C, CACNA1S, COL4A2, SRC, and CACNA1C were associated with bladder cancer risk. Two CCNE1 variants, rs8102137 and rs997669, from cell cycle pathways showed the strongest associations; the CCNE1 signal at 19q12 has already been reported in previous GWAS. These findings offer additional etiologic insights highlighting the specific genes and pathways associated with bladder cancer development. GSEA may be a complementary tool to GWAS to identify additional loci of cancer susceptibility.

  8. The role of prostatitis in prostate cancer: meta-analysis.

    Directory of Open Access Journals (Sweden)

    Junyi Jiang

    Full Text Available OBJECTIVE: Use systematic review methods to quantify the association between prostatitis and prostate cancer, under both fixed and random effects model. EVIDENCE ACQUISITION: Case control studies of prostate cancer with information on prostatitis history. All studies published between 1990-2012, were collected to calculate a pooled odds ratio. SELECTION CRITERIA: the selection criteria are as follows: human case control studies; published from May 1990 to July 2012; containing number of prostatitis, and prostate cancer cases. EVIDENCE SYNTHESIS: In total, 20 case control studies were included. A significant association between prostatitis and prostate cancer was found, under both fixed effect model (pooled OR=1.50, 95%CI: 1.39-1.62, and random effects model (OR=1.64, 95%CI: 1.36-1.98. Personal interview based case control studies showed a high level of association (fixed effect model: pooled OR=1.59, 95%CI: 1.47-1.73, random effects model: pooled OR= 1.87, 95%CI: 1.52-2.29, compared with clinical based studies (fixed effect model: pooled OR=1.05, 95%CI: 0.86-1.28, random effects model: pooled OR= 0.98, 95%CI: 0.67-1.45. Additionally, pooled ORs, were calculated for each decade. In a fixed effect model: 1990's: OR=1.58, 95% CI: 1.35-1.84; 2000's: OR=1.59, 95% CI: 1.40-1.79; 2010's: OR=1.37, 95% CI: 1.22-1.56. In a random effects model: 1990's: OR=1.98, 95% CI: 1.08-3.62; 2000's: OR=1.64, 95% CI: 1.23-2.19; 2010's: OR=1.34, 95% CI: 1.03-1.73. Finally a meta-analysis stratified by each country was conducted. In fixed effect models, U.S: pooled OR =1.45, 95%CI: 1.34-1.57; China: pooled OR =4.67, 95%CI: 3.08-7.07; Cuba: pooled OR =1.43, 95%CI: 1.00-2.04; Italy: pooled OR =0.61, 95%CI: 0.13-2.90. In random effects model, U.S: pooled OR=1.50, 95%CI: 1.25-1.80; China: pooled OR =4.67, 95%CI: 3.08-7.07; Cuba: pooled OR =1.43, 95%CI: 1.00-2.04; Italy: pooled OR =0.61, 95%CI: 0.13-2.90. CONCLUSIONS: the present meta-analysis provides the statistical

  9. Nonlinear structural analysis using integrated force method

    Indian Academy of Sciences (India)

    N R B Krishnam Raju; J Nagabhushanam


    Though the use of the integrated force method for linear investigations is well-recognised, no efforts were made to extend this method to nonlinear structural analysis. This paper presents the attempts to use this method for analysing nonlinear structures. General formulation of nonlinear structural analysis is given. Typically highly nonlinear bench-mark problems are considered. The characteristic matrices of the elements used in these problems are developed and later these structures are analysed. The results of the analysis are compared with the results of the displacement method. It has been demonstrated that the integrated force method is equally viable and efficient as compared to the displacement method.

  10. Cost Analysis: Methods and Realities. (United States)

    Cummings, Martin M.


    Argues that librarians need to be concerned with cost analysis of library functions and services because, in the allocation of resources, decision makers will favor library managers who demonstrate understanding of the relationships between costs and productive outputs. Factors that should be included in a reliable scheme for cost accounting are…

  11. Sphingosine kinase 1 and cancer: a systematic review and meta-analysis.

    Directory of Open Access Journals (Sweden)

    Yun Zhang

    Full Text Available BACKGROUND: Sphingosine kinase 1 (SK1 is a key regulator of the dynamic ceramide/sphingosine 1-phosphate rheostat balance and important in the pathological cancer genesis, progression, and metastasis processes. Many studies have demonstrated SK1 overexpressed in various cancers, but no meta-analysis has evaluated the relationship between SK1 and various cancers. METHODS: We retrieved relevant articles from the PubMed, EBSCO, ISI, and OVID databases. A pooled odds ratio (OR was used to assess the associations between SK1 expression and cancer; hazard ratios (HR were used for 5-year and overall survival. Review Manager 5.0 was used for the meta-analysis, and publication bias was evaluated with STATA 12.0 (Egger's test. RESULTS: Thirty-four eligible studies (n=4,673 patients were identified. SK1 positivity and high expression were significantly different between cancer, non-cancer, and benign tissues. SK1 mRNA and protein expression levels were elevated in the cancer tissues, compared with the normal tissues. SK1 positivity rates differed between various cancer types (lowest [27.3%] in estrogen receptor-positive breast cancer and highest [82.2%] in tongue squamous cell carcinoma. SK1 positivity and high expression were associated with 5-year survival; the HR was 1.86 (95% confidence interval [CI], 1.18-2.94 for breast cancer, 1.58 (1.08-2.31 for gastric cancer, and 2.68 (2.10-3.44 for other cancers; the total cancer HR was 2.21 (95% CI, 1.83-2.67; P < 0.00001. The overall survival HRs were 2.09 (95% CI, 1.35-3.22, 1.56 (1.08-2.25, and 2.62 (2.05-3.35 in breast, gastric, and other cancers, respectively. The total effect HR was 2.21 (95% CI, 1.83-2.66; P < 0.00001. CONCLUSIONS: SK1 positivity and high expression were significantly associated with cancer and a shorter 5-year and overall survival. SK1 positivity rates vary tremendously among the cancer types. It is necessary to further explore whether SK1 might be a predictive biomarker of outcomes in

  12. Gene Expression Analysis of Breast Cancer Progression (United States)


    Giri D, Chen B, Gerald W Molecular Diagnosis of Breast Cancer Therapeutic Biomarkers Using Oligonucleotide Arrays Abstract presentation USCAP 2005. 5...Bone Metastasis. Submitted Lal P, Donaton M, Girl D, Chen B, Gerald W Molecular Diagnosis of Breast Cancer Therapeutic Biomarkers Using Oligonucleotide

  13. Pathogenic Network Analysis Predicts Candidate Genes for Cervical Cancer

    Directory of Open Access Journals (Sweden)

    Yun-Xia Zhang


    Full Text Available Purpose. The objective of our study was to predicate candidate genes in cervical cancer (CC using a network-based strategy and to understand the pathogenic process of CC. Methods. A pathogenic network of CC was extracted based on known pathogenic genes (seed genes and differentially expressed genes (DEGs between CC and normal controls. Subsequently, cluster analysis was performed to identify the subnetworks in the pathogenic network using ClusterONE. Each gene in the pathogenic network was assigned a weight value, and then candidate genes were obtained based on the weight distribution. Eventually, pathway enrichment analysis for candidate genes was performed. Results. In this work, a total of 330 DEGs were identified between CC and normal controls. From the pathogenic network, 2 intensely connected clusters were extracted, and a total of 52 candidate genes were detected under the weight values greater than 0.10. Among these candidate genes, VIM had the highest weight value. Moreover, candidate genes MMP1, CDC45, and CAT were, respectively, enriched in pathway in cancer, cell cycle, and methane metabolism. Conclusion. Candidate pathogenic genes including MMP1, CDC45, CAT, and VIM might be involved in the pathogenesis of CC. We believe that our results can provide theoretical guidelines for future clinical application.

  14. Software Speeds Up Analysis of Breast Cancer Risk (United States)

    ... page: Software Speeds Up Analysis of Breast Cancer Risk: Study ... 22, 2016 THURSDAY, Sept. 22, 2016 (HealthDay News) -- Software that quickly analyzes mammograms and patient history to ...

  15. Hybrid methods for cybersecurity analysis :

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Warren Leon,; Dunlavy, Daniel M.


    Early 2010 saw a signi cant change in adversarial techniques aimed at network intrusion: a shift from malware delivered via email attachments toward the use of hidden, embedded hyperlinks to initiate sequences of downloads and interactions with web sites and network servers containing malicious software. Enterprise security groups were well poised and experienced in defending the former attacks, but the new types of attacks were larger in number, more challenging to detect, dynamic in nature, and required the development of new technologies and analytic capabilities. The Hybrid LDRD project was aimed at delivering new capabilities in large-scale data modeling and analysis to enterprise security operators and analysts and understanding the challenges of detection and prevention of emerging cybersecurity threats. Leveraging previous LDRD research e orts and capabilities in large-scale relational data analysis, large-scale discrete data analysis and visualization, and streaming data analysis, new modeling and analysis capabilities were quickly brought to bear on the problems in email phishing and spear phishing attacks in the Sandia enterprise security operational groups at the onset of the Hybrid project. As part of this project, a software development and deployment framework was created within the security analyst work ow tool sets to facilitate the delivery and testing of new capabilities as they became available, and machine learning algorithms were developed to address the challenge of dynamic threats. Furthermore, researchers from the Hybrid project were embedded in the security analyst groups for almost a full year, engaged in daily operational activities and routines, creating an atmosphere of trust and collaboration between the researchers and security personnel. The Hybrid project has altered the way that research ideas can be incorporated into the production environments of Sandias enterprise security groups, reducing time to deployment from months and

  16. Analysis of microsatellite instability in stool DNA of patients with colorectal cancer using denaturing high performance liquid chromatography

    Institute of Scientific and Technical Information of China (English)

    Seok-Byung Lim; Yong Shin; Sang-Geun Jang; Jae-Hyun Park; Jae-Gahb Park; Seung-Yong Jeong; Il-Jin Kim; Dae Yong Kim; Kyung Hae Jung; Hee Jin Chang; Hyo Seong Choi; Dae Kyung Sohn; Hio Chung Kang


    AIM: To evaluate the usefulness of denaturing high performance liquid chromatography (DHPLC) for analyzing microsatellite instability (MSI) status in stool DNA of patients with colorectal cancer.METHODS: A total of 80 cancer tissues from patients with primary sporadic colorectal tumor (proximal cancer:27, distal cancer: 53) and matched stool (which were employed for comparison with the tissues) were analyzed for MSI status in BAT 26. DNA samples extracted from stool were evaluated by nested polymerase chain reaction (PCR) and DHPLC for MSI analysis.RESULTS: Six cases (7.5%) of MSI were identified in BAT 26 from 80 cancer tissues. All the stool DNA samples from patients whose cancer tissue showed MSI also displayed MSI in BAT 26.CONCLUSION: As MSI is one of the established fecal DNA markers to screen colorectal cancer, we propose to use DHPLC for the MSI analysis in fecal DNA.

  17. Vitamin D and Lung Cancer Risk: A Comprehensive Review and Meta-Analysis

    Directory of Open Access Journals (Sweden)

    Liqun Zhang


    Full Text Available Background/Aim: Vitamin D has been suggested to have important roles against cancer development. There were several published studies on the association between vitamin D and lung cancer risk, but not conclusive results were available. Methods: To clarify the role of vitamin D in lung carcinogenesis, we performed a comprehensive review of the literature and a meta-analysis to evaluate the association of serum vitamin D levels and dietary vitamin D intake with lung cancer risk. Twelve studies (9 prospective cohort and 3 nested case-control studies with a total of 288,778 individuals were included. The summary relative risk (RR with 95% confidence interval (CI was used to assess lung cancer risk. Results: Meta-analysis of total 12 studies showed that RR for the association of high vitamin D status with lung cancer was 0.84 (95%CI 0.78-0.90, P Conclusion: Current data suggest an inverse association between serum vitamin D and lung cancer risk. Further studies are needed to investigate the effect of vitamin D intake on lung cancer risk and to evaluate whether vitamin D supplementation can prevent lung cancer.

  18. Bioinformatics analysis of breast cancer bone metastasis related gene-CXCR4

    Institute of Scientific and Technical Information of China (English)

    Heng-Wei Zhang; Xian-Fu Sun; Ya-Ning He; Jun-Tao Li; Xu-Hui Guo; Hui Liu


    Objective: To analyze breast cancer bone metastasis related gene-CXCR4. Methods: This research screened breast cancer bone metastasis related genes by high-flux gene chip. Results:It was found that the expressions of 396 genes were different including 165 up-regulations and 231 down-regulations. The expression of chemokine receptor CXCR4 was obviously up-regulated in the tissue with breast cancer bone metastasis. Compared with the tissue without bone metastasis, there was significant difference, which indicated that CXCR4 played a vital role in breast cancer bone metastasis. Conclusions: The bioinformatics analysis of CXCR4 can provide a certain basis for the occurrence and diagnosis of breast cancer bone metastasis, target gene therapy and evaluation of prognosis.

  19. Fingerprinting Breast Cancer vs. Normal Mammary Cells by Mass Spectrometric Analysis of Volatiles (United States)

    He, Jingjing; Sinues, Pablo Martinez-Lozano; Hollmén, Maija; Li, Xue; Detmar, Michael; Zenobi, Renato


    There is increasing interest in the development of noninvasive diagnostic methods for early cancer detection, to improve the survival rate and quality of life of cancer patients. Identification of volatile metabolic compounds may provide an approach for noninvasive early diagnosis of malignant diseases. Here we analyzed the volatile metabolic signature of human breast cancer cell lines versus normal human mammary cells. Volatile compounds in the headspace of conditioned culture medium were directly fingerprinted by secondary electrospray ionization-mass spectrometry. The mass spectra were subsequently treated statistically to identify discriminating features between normal vs. cancerous cell types. We were able to classify different samples by using feature selection followed by principal component analysis (PCA). Additionally, high-resolution mass spectrometry allowed us to propose their chemical structures for some of the most discriminating molecules. We conclude that cancerous cells can release a characteristic odor whose constituents may be used as disease markers.

  20. c-src activating mutation analysis in Chinese patients with colorectal cancer

    Institute of Scientific and Technical Information of China (English)

    Ye-Xiong Tan; Han-Tao Wang; Peng Zhang; Zhong-Hua Yan; Guan-Long Dai; Meng-Chao Wu; Hong-Yang Wang


    AIM: To investigate the occurrence of cellular src (c-src)activating mutation at codon 531 in colorectal cancer patients from Chinese mainland.METHODS: Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay followed by sequencing and single-strand conformation polymorphism analysis were carried out to screen 110 samples of primary colorectal cancer and 20 colorectal liver metastases.RESULTS: Only one sample showed PCR-RFLP-positive results and carried somatic codon 531 mutations. No additional mutation of c-src exon 12 was found.CONCLUSION: c-src codon 531 mutation in colorectal cancer is not the cause of c-src activation.

  1. Breast cancer research output, 1945-2008: a bibliometric and density-equalizing analysis

    LENUS (Irish Health Repository)

    Glynn, Ronan W


    Abstract Introduction Breast cancer is the most common form of cancer among women, with an estimated 194,280 new cases diagnosed in the United States in 2009 alone. The primary aim of this work was to provide an in-depth evaluation of research yield in breast cancer from 1945 to 2008, using large-scale data analysis, the employment of bibliometric indicators of production and quality, and density-equalizing mapping. Methods Data were retrieved from the Web of Science (WOS) Science Citation Expanded database; this was searched using the Boolean operator, \\'OR\\

  2. Cell cycle genes and ovarian cancer susceptibility: a tagSNP analysis

    DEFF Research Database (Denmark)

    Cunningham, J M; Vierkant, R A; Sellers, T A;


    BACKGROUND: Dysregulation of the cell cycle is a hallmark of many cancers including ovarian cancer, a leading cause of gynaecologic cancer mortality worldwide. METHODS: We examined single nucleotide polymorphisms (SNPs) (n=288) from 39 cell cycle regulation genes, including cyclins, cyclin...... in a replication population, and the association remained suggestive in the combined analysis [OR(BB vs AA) 1.59 (1.08-2.34), P=0.02]. No other SNP associations remained suggestive in the replication populations. CONCLUSION: ABL1 has been implicated in multiple processes including cell division, cell adhesion...

  3. Content validity across methods of malnutrition assessment in patients with cancer is limited

    NARCIS (Netherlands)

    Sealy, Martine J.; Nijholt, Willemke; Stuiver, Martijn M.; van der Berg, Marit M.; Roodenburg, Jan L. N.; Schans, van der Cees P.; Ottery, Faith D.; Jager-Wittenaar, Harriet


    Objective: To identify malnutrition assessment methods in cancer patients and assess their content validity based on internationally accepted definitions for malnutrition. Study Design and Setting: Systematic review of studies in cancer patients that operationalized malnutrition as a variable, publi

  4. The Feasibility of Societal Cost Equivalence between Robotic Hysterectomy and Alternate Hysterectomy Methods for Endometrial Cancer

    Directory of Open Access Journals (Sweden)

    Neel T. Shah


    Full Text Available Objectives. We assess whether it is feasible for robotic hysterectomy for endometrial cancer to be less expensive to society than traditional laparoscopic hysterectomy or abdominal hysterectomy. Methods. We performed a retrospective cohort analysis of patient characteristics, operative times, complications, and hospital charges from all (=234 endometrial cancer patients who underwent hysterectomy in 2009 at our hospital. Per patient costs of each hysterectomy method were examined from the societal perspective. Sensitivity analysis and Monte Carlo simulation were performed using a cost-minimization model. Results. 40 (17.1% of hysterectomies for endometrial cancer were robotic, 91 (38.9%, were abdominal, and 103 (44.0% were laparoscopic. 96.3% of the variation in operative cost between patients was predicted by operative time (=0.963, <0.01. Mean operative time for robotic hysterectomy was significantly longer than other methods (<0.01. Abdominal hysterectomy was consistently the most expensive while the traditional laparoscopic approach was consistently least expensive. The threshold in operative time that makes robotic hysterectomy cost equivalent to the abdominal approach is within the range of our experience. Conclusion. It is feasible for robotic hysterectomy to be less expensive than abdominal hysterectomy, but unlikely for robotic hysterectomy to be less expensive than traditional laparoscopy.

  5. Probabilistic Analysis Methods for Hybrid Ventilation

    DEFF Research Database (Denmark)

    Brohus, Henrik; Frier, Christian; Heiselberg, Per

    This paper discusses a general approach for the application of probabilistic analysis methods in the design of ventilation systems. The aims and scope of probabilistic versus deterministic methods are addressed with special emphasis on hybrid ventilation systems. A preliminary application...

  6. The Functional Methods of Discourse Analysis

    Institute of Scientific and Technical Information of China (English)



    From the macroscopic angle of function, methods of discourse analysis are clarified to find out two important methods in pragmatics and through which will better used in the understanding of discourse.

  7. Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012. (United States)

    Ferlay, Jacques; Soerjomataram, Isabelle; Dikshit, Rajesh; Eser, Sultan; Mathers, Colin; Rebelo, Marise; Parkin, Donald Maxwell; Forman, David; Bray, Freddie


    Estimates of the worldwide incidence and mortality from 27 major cancers and for all cancers combined for 2012 are now available in the GLOBOCAN series of the International Agency for Research on Cancer. We review the sources and methods used in compiling the national cancer incidence and mortality estimates, and briefly describe the key results by cancer site and in 20 large "areas" of the world. Overall, there were 14.1 million new cases and 8.2 million deaths in 2012. The most commonly diagnosed cancers were lung (1.82 million), breast (1.67 million), and colorectal (1.36 million); the most common causes of cancer death were lung cancer (1.6 million deaths), liver cancer (745,000 deaths), and stomach cancer (723,000 deaths).

  8. Earth analysis methods, subsurface feature detection methods, earth analysis devices, and articles of manufacture (United States)

    West, Phillip B.; Novascone, Stephen R.; Wright, Jerry P.


    Earth analysis methods, subsurface feature detection methods, earth analysis devices, and articles of manufacture are described. According to one embodiment, an earth analysis method includes engaging a device with the earth, analyzing the earth in a single substantially lineal direction using the device during the engaging, and providing information regarding a subsurface feature of the earth using the analysis.

  9. Infinitesimal methods of mathematical analysis

    CERN Document Server

    Pinto, J S


    This modern introduction to infinitesimal methods is a translation of the book Métodos Infinitesimais de Análise Matemática by José Sousa Pinto of the University of Aveiro, Portugal and is aimed at final year or graduate level students with a background in calculus. Surveying modern reformulations of the infinitesimal concept with a thoroughly comprehensive exposition of important and influential hyperreal numbers, the book includes previously unpublished material on the development of hyperfinite theory of Schwartz distributions and its application to generalised Fourier transforms and harmon

  10. Novel Diagnostic Method for Personalized Treatment of Cancer

    DEFF Research Database (Denmark)

    Zulfiqar, Azeem

    Point-Of-Care (POC) devices, due to their better portability and easy-to-use functions, have already found their way into the domestic house hold appliances. The technologies developed for these devices have enabled the mankind to monitor the health related problems at home such as the blood...... relies on highly expensive tools e.g. e-beam lithography, and expensive substrates e.g. Silicon-On-Insulator (SOI) which poses hurdle in cheap and fast production of the devices that can be used for both research purposes and for domestic use. In this project, a novel fabrication method, using in......-microfluidic system on top of SiNW is demonstrated. The durability of the microfluidic system has also been tested. In the third part, different functionalization methods are explained and used to demonstrate the bio sensing on the SiNW sensor. The detection of cancer biomarker is also tested on these devices. Lastly...

  11. Meta-Analysis of Massage Therapy on Cancer Pain. (United States)

    Lee, Sook-Hyun; Kim, Jong-Yeop; Yeo, Sujung; Kim, Sung-Hoon; Lim, Sabina


    Cancer pain is the most common complaint among patients with cancer. Conventional treatment does not always relieve cancer pain satisfactorily. Therefore, many patients with cancer have turned to complementary therapies to help them with their physical, emotional, and spiritual well-being. Massage therapy is increasingly used for symptom relief in patients with cancer. The current study aimed to investigate by meta-analysis the effects of massage therapy for cancer patients experiencing pain. Nine electronic databases were systematically searched for studies published through August 2013 in English, Chinese, and Korean. Methodological quality was assessed using the Physiotherapy Evidence Database (PEDro) and Cochrane risk-of-bias scales. Twelve studies, including 559 participants, were used in the meta-analysis. In 9 high-quality studies based on the PEDro scale (standardized mean difference, -1.24; 95% confidence interval, -1.72 to -0.75), we observed reduction in cancer pain after massage. Massage therapy significantly reduced cancer pain compared with no massage treatment or conventional care (standardized mean difference, -1.25; 95% confidence interval, -1.63 to -0.87). Our results indicate that massage is effective for the relief of cancer pain, especially for surgery-related pain. Among the various types of massage, foot reflexology appeared to be more effective than body or aroma massage. Our meta-analysis indicated a beneficial effect of massage for relief of cancer pain. Further well-designed, large studies with longer follow-up periods are needed to be able to draw firmer conclusions regarding the effectiveness.

  12. Single-cell analysis in cancer genomics (United States)

    Saadatpour, Assieh; Lai, Shujing; Guo, Guoji; Yuan, Guo-Cheng


    Genetic changes and environmental differences result in cellular heterogeneity among cancer cells within the same tumor, thereby complicating treatment outcomes. Recent advances in single-cell technologies have opened new avenues to characterize the intra-tumor cellular heterogeneity, identify rare cell types, measure mutation rates, and, ultimately, guide diagnosis and treatment. In this paper, we review the recent single-cell technological and computational advances at the genomic, transcriptomic, and proteomic levels, and discuss their applications in cancer research. PMID:26450340

  13. What does cancer treatment look like in consumer cancer magazines? An exploratory analysis of photographic content in consumer cancer magazines. (United States)

    Phillips, Selene G; Della, Lindsay J; Sohn, Steve H


    In an exploratory analysis of several highly circulated consumer cancer magazines, the authors evaluated congruency between visual images of cancer patients and target audience risk profile. The authors assessed 413 images of cancer patients/potential patients for demographic variables such as age, gender, and ethnicity/race. They compared this profile with actual risk statistics. The images in the magazines are considerably younger, more female, and more White than what is indicated by U.S. cancer risk statistics. The authors also assessed images for visual signs of cancer testing/diagnosis and treatment. Few individuals show obvious signs of cancer treatment (e.g., head scarves, skin/nail abnormalities, thin body types). Most images feature healthier looking people, some actively engaged in construction work, bicycling, and yoga. In contrast, a scan of the editorial content showed that nearly two thirds of the articles focus on treatment issues. To explicate the implications of this imagery-text discontinuity on readers' attention and cognitive processing, the authors used constructs from information processing and social identity theories. On the basis of these models/theories, the authors provide recommendations for consumer cancer magazines, suggesting that the imagery be adjusted to reflect cancer diagnosis realities for enhanced message attention and comprehension.

  14. Application of Parametric Models of Survival Analysis in Determining the Cancer Influencing Factors in Patients with Thyroid Nodules


    J.Yazdani Charati; O. Akha; AR Baghestani; F. Khosravi; Y Kavyani Charati


    Background & aim: One of the most common clinical problems among individuals is thyroid nodule diseases which are characterized by one or more nodules in the thyroid and are usually benign. It can be said that thyroid cancer is the most common endocrine cancer worldwide. This study aimed to determine the risk factors for cancer in patients with thyroid nodule in Mazandaran province,Iran, using parametric survival analysis. Methods: In the present historical cohort study, 26,730 patients w...

  15. Genomic analysis of epithelial ovarian cancer

    Institute of Scientific and Technical Information of China (English)

    John Farley; Laurent L Ozbun; Michael J Birrer


    Ovarian cancer is a major health problem for women in the United States.Despite evidence of considerable heterogeneity,most cases of ovarian cancer are treated in a similar fashion.The molecular basis for the clinicopathologic characteristics of these tumors remains poorly defined.Whole genome expression profiling is a genomic tool,which can identify dysregulated genes and uncover unique sub-classes of tumors.The application of this technology to ovarian cancer has provided a solid molecular basis for differences in histology and grade of ovarian tumors.Differentially expressed genes identified pathways implicated in cell proliferation,invasion,motility,chromosomal instability,and gene silencing and provided new insights into the origin and potential treatment of these cancers.The added knowledge provided by global gene expression profiling should allow for a more rational treatment of ovarian cancers.These techniques are leading to a paradigm shift from empirical treatment to an individually tailored approach.This review summarizes the new genomic data on epithelial ovarian cancers of different histology and grade and the impact it will have on our understanding and treatment of this disease.

  16. Prognostic value of PLR in various cancers: a meta-analysis.

    Directory of Open Access Journals (Sweden)

    Xin Zhou

    Full Text Available BACKGROUND: Recently, more and more studies investigated the association of inflammation parameters such as the Platelet Lymphocyte Ratio (PLR and the prognosis of various cancers. However, the prognostic role of PLR in cancer remains controversial. METHODS: We conducted a meta-analysis of published studies to evaluate the prognostic value of PLR in various cancers. In order to investigate the association between PLR and overall survival (OS, the hazard ratio (HR and its 95% confidence interval (CI were calculated. RESULTS: A total of 13,964 patients from 26 studies were included in the analysis. The summary results showed that elevated PLR was a negative predictor for OS with HR of 1.60 (95%CI: 1.35-1.90; Pheterogeneity <0.001. Subgroup analysis revealed that increased PLR was a negative prognostic marker in patients with gastric cancer (HR = 1.35, 95%CI: 0.80-2.25, Pheterogeneity = 0.011, colorectal cancer (HR = 1.65, 95%CI: 1.33-2.05, Pheterogeneity = 0.995, hepatocellular carcinoma (HR = 3.07, 95% CI: 2.04-4.62, Pheterogeneity = 0.133, ovarian cancer (HR = 1.57, 95%CI: 1.07-2.31, Pheterogeneity = 0.641 and non-small cell lung cancer (NSCLC (HR = 1.85, 95% CI: 1.42-2.41, Pheterogeneity = 0.451 except for pancreatic cancer (HR = 1.00, 95%CI: 0.92-1.09, Pheterogeneity = 0.388. CONCLUSION: The meta-analysis demonstrated that PLR could act as a significant biomarker in the prognosis of various cancers.

  17. The correlation of contrast-enhanced ultrasound and MRI perfusion quantitative analysis in rabbit VX2 liver cancer. (United States)

    Xiang, Zhiming; Liang, Qianwen; Liang, Changhong; Zhong, Guimian


    Our objective is to explore the value of liver cancer contrast-enhanced ultrasound (CEUS) and MRI perfusion quantitative analysis in liver cancer and the correlation between these two analysis methods. Rabbit VX2 liver cancer model was established in this study. CEUS was applied. Sono Vue was applied in rabbits by ear vein to dynamically observe and record the blood perfusion and changes in the process of VX2 liver cancer and surrounding tissue. MRI perfusion quantitative analysis was used to analyze the mean enhancement time and change law of maximal slope increasing, which were further compared with the pathological examination results. Quantitative indicators of liver cancer CEUS and MRI perfusion quantitative analysis were compared, and the correlation between them was analyzed by correlation analysis. Rabbit VX2 liver cancer model was successfully established. CEUS showed that time-intensity curve of rabbit VX2 liver cancer showed "fast in, fast out" model while MRI perfusion quantitative analysis showed that quantitative parameter MTE of tumor tissue increased and MSI decreased: the difference was statistically significant (P 0.05). However, the quantitative parameter of them were significantly positively correlated (P liver cancer lesion and surrounding liver parenchyma, and the quantitative parameters of them are correlated. The combined application of both is of importance in early diagnosis of liver cancer.

  18. CHRNA5 risk variant predicts delayed smoking cessation and earlier lung cancer diagnosis--a meta-analysis

    NARCIS (Netherlands)

    Chen, L.S.; Hung, R.J.; Baker, T.; Horton, A.; Culverhouse, R.; Saccone, N.; Cheng, I.; Deng, B.; Han, Y.; Hansen, H.M.; Horsman, J.; Kim, C.; Lutz, S.; Rosenberger, A.; Aben, K.K.H.; Andrew, A.S.; Breslau, N.; Chang, S.C.; Dieffenbach, A.K.; Dienemann, H.; Frederiksen, B.; Han, J.; Hatsukami, D.K.; Johnson, E.O.; Pande, M.; Wrensch, M.R.; McLaughlin, J.; Skaug, V.; Heijden, H.F. van der; Wampfler, J.; Wenzlaff, A.; Woll, P.; Zienolddiny, S.; Bickeboller, H.; Brenner, H.; Duell, E.J.; Haugen, A.; Heinrich, J.; Hokanson, J.E.; Hunter, D.J.; Kiemeney, B.; Lazarus, P.; Marchand, L. Le; Liu, G.; Mayordomo, J.; Risch, A.; Schwartz, A.G.; Teare, D.; Wu, X.; Wiencke, J.K.; Yang, P.; Zhang, Z.F.; Spitz, M.R.; Kraft, P.; Amos, C.I.; Bierut, L.J.


    BACKGROUND: Recent meta-analyses show strong evidence of associations among genetic variants in CHRNA5 on chromosome 15q25, smoking quantity, and lung cancer. This meta-analysis tests whether the CHRNA5 variant rs16969968 predicts age of smoking cessation and age of lung cancer diagnosis. METHODS: M

  19. Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes

    Directory of Open Access Journals (Sweden)

    Eils Roland


    Full Text Available Abstract Background The extensive use of DNA microarray technology in the characterization of the cell transcriptome is leading to an ever increasing amount of microarray data from cancer studies. Although similar questions for the same type of cancer are addressed in these different studies, a comparative analysis of their results is hampered by the use of heterogeneous microarray platforms and analysis methods. Results In contrast to a meta-analysis approach where results of different studies are combined on an interpretative level, we investigate here how to directly integrate raw microarray data from different studies for the purpose of supervised classification analysis. We use median rank scores and quantile discretization to derive numerically comparable measures of gene expression from different platforms. These transformed data are then used for training of classifiers based on support vector machines. We apply this approach to six publicly available cancer microarray gene expression data sets, which consist of three pairs of studies, each examining the same type of cancer, i.e. breast cancer, prostate cancer or acute myeloid leukemia. For each pair, one study was performed by means of cDNA microarrays and the other by means of oligonucleotide microarrays. In each pair, high classification accuracies (> 85% were achieved with training and testing on data instances randomly chosen from both data sets in a cross-validation analysis. To exemplify the potential of this cross-platform classification analysis, we use two leukemia microarray data sets to show that important genes with regard to the biology of leukemia are selected in an integrated analysis, which are missed in either single-set analysis. Conclusion Cross-platform classification of multiple cancer microarray data sets yields discriminative gene expression signatures that are found and validated on a large number of microarray samples, generated by different laboratories and

  20. Automated analysis of image mammogram for breast cancer diagnosis (United States)

    Nurhasanah, Sampurno, Joko; Faryuni, Irfana Diah; Ivansyah, Okto


    Medical imaging help doctors in diagnosing and detecting diseases that attack the inside of the body without surgery. Mammogram image is a medical image of the inner breast imaging. Diagnosis of breast cancer needs to be done in detail and as soon as possible for determination of next medical treatment. The aim of this work is to increase the objectivity of clinical diagnostic by using fractal analysis. This study applies fractal method based on 2D Fourier analysis to determine the density of normal and abnormal and applying the segmentation technique based on K-Means clustering algorithm to image abnormal for determine the boundary of the organ and calculate the area of organ segmentation results. The results show fractal method based on 2D Fourier analysis can be used to distinguish between the normal and abnormal breast and segmentation techniques with K-Means Clustering algorithm is able to generate the boundaries of normal and abnormal tissue organs, so area of the abnormal tissue can be determined.

  1. Method for detecting, screening and/or montoring a cancer in individual

    DEFF Research Database (Denmark)


    The invention relates to a method for screening and/or detecting and/or monitoring a cancer in an individual, said method comprising determining a first parameter represented by the concentration of TIMP-1 in at least one excreta, e.g. saliva, from the individual. The invention provides a method...... that without the need to use a blood sample is suitable for facilitating the early diagnosis of a cancer, monitoring the recurrence of a cancer, and/or monitoring the status of a cancer or the effect of cancer treatment in an individual....

  2. Probabilistic structural analysis by extremum methods (United States)

    Nafday, Avinash M.


    The objective is to demonstrate discrete extremum methods of structural analysis as a tool for structural system reliability evaluation. Specifically, linear and multiobjective linear programming models for analysis of rigid plastic frames under proportional and multiparametric loadings, respectively, are considered. Kinematic and static approaches for analysis form a primal-dual pair in each of these models and have a polyhedral format. Duality relations link extreme points and hyperplanes of these polyhedra and lead naturally to dual methods for system reliability evaluation.

  3. Coffee consumption and risk of breast cancer: an up-to-date meta-analysis.

    Directory of Open Access Journals (Sweden)

    Xiu Juan Li

    Full Text Available OBJECTIVES: This updated meta-analysis was conducted to assess the association between coffee consumption and breast cancer risk. METHODS: We conducted a systematic search updated July 2012 to identify observational studies providing quantitative estimates for breast cancer risk in relation to coffee consumption. Pooled relative risks (RRs with 95% confidence intervals (CIs were calculated using a random-effects model, and generalized least square trend estimation was used to assess dose-response relationships. RESULTS: A total of 26 studies (16 cohort and 10 case-control studies on coffee intake with 49497 breast cancer cases were included in the meta-analysis. The pooled RR showed a borderline significant influence of highest coffee consumption (RR = 0.96; 95% CI 0.93-1.00, low-to moderate coffee consumption (RR = 0.99; 95% CI 0.95-1.04, or an increment of 2 cups/day of coffee consumption (RR = 0.98; 95% CI 0.97-1.00 on the risk of breast cancer. In stratified analysis, a significant inverse association was observed in ER-negative subgroup. However, no significant association was noted in the others. CONCLUSIONS: Our findings suggest that increased coffee intake is not associated with a significantly reduced risk of breast cancer, but we observe an inverse association in ER-negative subgroup analysis. More large studies are needed to determine subgroups to obtain more valuable data on coffee drinking and breast cancer risk.

  4. Up-to-date and precise estimates of cancer patient survival: model-based period analysis. (United States)

    Brenner, Hermann; Hakulinen, Timo


    Monitoring of progress in cancer patient survival by cancer registries should be as up-to-date as possible. Period analysis has been shown to provide more up-to-date survival estimates than do traditional methods of survival analysis. However, there is a trade-off between up-to-dateness and the precision of period estimates, in that increasing the up-to-dateness of survival estimates by restricting the analysis to a relatively short, recent time period, such as the most recent calendar year for which cancer registry data are available, goes along with a loss of precision. The authors propose a model-based approach to maximize the up-to-dateness of period estimates at minimal loss of precision. The approach is illustrated for monitoring of 5-year relative survival of patients diagnosed with one of 20 common forms of cancer in Finland between 1953 and 2002 by use of data from the nationwide Finnish Cancer Registry. It is shown that the model-based approach provides survival estimates that are as up-to-date as the most up-to-date conventional period estimates and at the same time much more precise than the latter. The modeling approach may further enhance the use of period analysis for deriving up-to-date cancer survival rates.

  5. Sensitivity Analysis Using Simple Additive Weighting Method

    Directory of Open Access Journals (Sweden)

    Wayne S. Goodridge


    Full Text Available The output of a multiple criteria decision method often has to be analyzed using some sensitivity analysis technique. The SAW MCDM method is commonly used in management sciences and there is a critical need for a robust approach to sensitivity analysis in the context that uncertain data is often present in decision models. Most of the sensitivity analysis techniques for the SAW method involve Monte Carlo simulation methods on the initial data. These methods are computationally intensive and often require complex software. In this paper, the SAW method is extended to include an objective function which makes it easy to analyze the influence of specific changes in certain criteria values thus making easy to perform sensitivity analysis.

  6. Assessment of breast cancer tumour size using six different methods

    Energy Technology Data Exchange (ETDEWEB)

    Meier-Meitinger, Martina; Uder, Michael; Schulz-Wendtland, Ruediger; Adamietz, Boris [Erlangen University Hospital, Institute of Diagnostic Radiology, Erlangen (Germany); Haeberle, Lothar; Fasching, Peter A.; Bani, Mayada R.; Heusinger, Katharina; Beckmann, Matthias W. [Erlangen University Hospital, University Breast Center, Department of Gynecology and Obstetrics, Erlangen (Germany); Wachter, David [Erlangen University Hospital, Institute of Pathology, Erlangen (Germany)


    Tumour size estimates using mammography (MG), conventional ultrasound (US), compound imaging (CI) and real-time elastography (RTE) were compared with histopathological specimen sizes. The largest diameters of 97 malignant breast lesions were measured. Two US and CI measurements were made: US1/CI1 (hypoechoic nucleus only) and US2/CI2 (hypoechoic nucleus plus hyperechoic halo). Measurements were compared with histopathological tumour sizes using linear regression and Bland-Altman plots. Size prediction was best with ultrasound (US/CI/RTE: R{sup 2} 0.31-0.36); mammography was poorer (R{sup 2} = 0.19). The most accurate method was US2, while US1 and CI1 were poorest. Bland-Altman plots showed better size estimation with US2, CI2 and RTE, with low variation, while mammography showed greatest variability. Smaller tumours were better assessed than larger ones. CI2 and US2 performed best for ductal tumours and RTE for lobular cancers. Tumour size prediction accuracy did not correlate significantly with breast density, but on MG tumours were more difficult to detect in high-density tissue. The size of ductal tumours is best predicted with US2 and CI2, while for lobular cancers RTE is best. Hyperechoic tumour surroundings should be included in US and CI measurements and RTE used as an additional technique in the clinical staging process. (orig.)

  7. Artificial Neural Network Analysis in Preclinical Breast Cancer

    Directory of Open Access Journals (Sweden)

    Gholamreza Motalleb


    Full Text Available Objective: In this study, artificial neural network (ANN analysis of virotherapy in preclinical breast cancer was investigated.Materials and Methods: In this research article, a multilayer feed-forward neural network trained with an error back-propagation algorithm was incorporated in order to develop a predictive model. The input parameters of the model were virus dose, week and tamoxifen citrate, while tumor weight was included in the output parameter. Two different training algorithms, namely quick propagation (QP and Levenberg-Marquardt (LM, were used to train ANN.Results: The results showed that the LM algorithm, with 3-9-1 arrangement is more efficient compared to QP. Using LM algorithm, the coefficient of determination (R2 between the actual and predicted values was determined as 0.897118 for all data.Conclusion: It can be concluded that this ANN model may provide good ability to predict the biometry information of tumor in preclinical breast cancer virotherapy. The results showed that the LM algorithm employed by Neural Power software gave the better performance compared with the QP and virus dose, and it is more important factor compared to tamoxifen and time (week.

  8. Multi-class texture analysis in colorectal cancer histology (United States)

    Kather, Jakob Nikolas; Weis, Cleo-Aron; Bianconi, Francesco; Melchers, Susanne M.; Schad, Lothar R.; Gaiser, Timo; Marx, Alexander; Zöllner, Frank Gerrit


    Automatic recognition of different tissue types in histological images is an essential part in the digital pathology toolbox. Texture analysis is commonly used to address this problem; mainly in the context of estimating the tumour/stroma ratio on histological samples. However, although histological images typically contain more than two tissue types, only few studies have addressed the multi-class problem. For colorectal cancer, one of the most prevalent tumour types, there are in fact no published results on multiclass texture separation. In this paper we present a new dataset of 5,000 histological images of human colorectal cancer including eight different types of tissue. We used this set to assess the classification performance of a wide range of texture descriptors and classifiers. As a result, we found an optimal classification strategy that markedly outperformed traditional methods, improving the state of the art for tumour-stroma separation from 96.9% to 98.6% accuracy and setting a new standard for multiclass tissue separation (87.4% accuracy for eight classes). We make our dataset of histological images publicly available under a Creative Commons license and encourage other researchers to use it as a benchmark for their studies.

  9. Text analysis methods, text analysis apparatuses, and articles of manufacture (United States)

    Whitney, Paul D; Willse, Alan R; Lopresti, Charles A; White, Amanda M


    Text analysis methods, text analysis apparatuses, and articles of manufacture are described according to some aspects. In one aspect, a text analysis method includes accessing information indicative of data content of a collection of text comprising a plurality of different topics, using a computing device, analyzing the information indicative of the data content, and using results of the analysis, identifying a presence of a new topic in the collection of text.

  10. Physical therapy methods in the treatment and rehabilitation of cancer patients (United States)

    Kucherova, T. Ya.; Velikaya, V. V.; Gribova, O. V.; Startseva, Zh. A.; Choinzonov, E. L.; Tuzikov, S. A.; Vusik, M. V.; Doroshenko, A. V.


    The results of the effective use of magnetic laser therapy in the treatment and rehabilitation of cancer patients were presented. The effect of magnetic-laser therapy in the treatment of radiation-induced reactions in the patients with head and neck cancer and in the patients with breast cancer was analyzed. High efficiency of lymphedema and lymphorrhea treatment in the postoperative period in the patients with breast cancer was proved. The results of rehabilitation of the patients with gastric cancer after surgical treatment were presented. These data indicate a high effectiveness of different physical methods of treatment and rehabilitation of cancer patients.

  11. Polyamine Metabolites Profiling for Characterization of Lung and Liver Cancer Using an LC-Tandem MS Method with Multiple Statistical Data Mining Strategies: Discovering Potential Cancer Biomarkers in Human Plasma and Urine

    Directory of Open Access Journals (Sweden)

    Huarong Xu


    Full Text Available Polyamines, one of the most important kind of biomarkers in cancer research, were investigated in order to characterize different cancer types. An integrative approach which combined ultra-high performance liquid chromatography—tandem mass spectrometry detection and multiple statistical data processing strategies including outlier elimination, binary logistic regression analysis and cluster analysis had been developed to discover the characteristic biomarkers of lung and liver cancer. The concentrations of 14 polyamine metabolites in biosamples from lung (n = 50 and liver cancer patients (n = 50 were detected by a validated UHPLC-MS/MS method. Then the concentrations were converted into independent variables to characterize patients of lung and liver cancer by binary logic regression analysis. Significant independent variables were regarded as the potential biomarkers. Cluster analysis was engaged for further verifying. As a result, two values was discovered to identify lung and liver cancer, which were the product of the plasma concentration of putrescine and spermidine; and the ratio of the urine concentration of S-adenosyl-l-methionine and N-acetylspermidine. Results indicated that the established advanced method could be successfully applied to characterize lung and liver cancer, and may also enable a new way of discovering cancer biomarkers and characterizing other types of cancer.

  12. Polyamine Metabolites Profiling for Characterization of Lung and Liver Cancer Using an LC-Tandem MS Method with Multiple Statistical Data Mining Strategies: Discovering Potential Cancer Biomarkers in Human Plasma and Urine. (United States)

    Xu, Huarong; Liu, Ran; He, Bosai; Bi, Cathy Wenchuan; Bi, Kaishun; Li, Qing


    Polyamines, one of the most important kind of biomarkers in cancer research, were investigated in order to characterize different cancer types. An integrative approach which combined ultra-high performance liquid chromatography-tandem mass spectrometry detection and multiple statistical data processing strategies including outlier elimination, binary logistic regression analysis and cluster analysis had been developed to discover the characteristic biomarkers of lung and liver cancer. The concentrations of 14 polyamine metabolites in biosamples from lung (n = 50) and liver cancer patients (n = 50) were detected by a validated UHPLC-MS/MS method. Then the concentrations were converted into independent variables to characterize patients of lung and liver cancer by binary logic regression analysis. Significant independent variables were regarded as the potential biomarkers. Cluster analysis was engaged for further verifying. As a result, two values was discovered to identify lung and liver cancer, which were the product of the plasma concentration of putrescine and spermidine; and the ratio of the urine concentration of S-adenosyl-l-methionine and N-acetylspermidine. Results indicated that the established advanced method could be successfully applied to characterize lung and liver cancer, and may also enable a new way of discovering cancer biomarkers and characterizing other types of cancer.

  13. A meta-analysis of the association between Chlamydia pneumoniae infection and lung cancer risk

    Directory of Open Access Journals (Sweden)

    X Hua-Feng


    Full Text Available Objective: The association between Chlamydia pneumoniae infection and lung cancer risk was not clear with small number of cases in each study. The aim of this meta-analysis was to evaluate the correlation between pneumonia infection and lung cancer risk by pooling the open published papers. Materials and Methods: We searched the electronic databases of Medline, EMBASE, Web of Science, and China National Knowledge Infrastructure databases for publications related to the association between pneumonia infection and lung cancer risk. Odds ratio (OR and its 95% confidence interval (95% CI was used to assess the correlation. The data were pooled by Stata11.0 software (Stata Corporation, College Station, TX, USA. Results: Thirteen publications, involving 2549 lung cancer patients and 2764 controls were included in this meta-analysis. The pooled results indicated that the C. pneumoniae infection significant increased the risk of lung cancer OR = 2.07 (95% CI: 1.43–2.99 by random effect model. And for serum IgG, 12 publications reported the IgG positive rate in lung cancer patients and relative healthy controls. The pooled OR was 2.22 (95% CI: 1.41–3.50 by using the random effects model which indicated that the IgG positive rate was significantly higher in lung cancer patients than that of healthy controls. The sensitivity analysis indicated the pooled OR was not sensitive to a single study. However, Begger's funnel plot and Egger's line regression analysis indicated significant publications bias for this meta-analysis. Conclusions: According to the present published data, C. pneumoniae infection may increase the risk of lung cancer. However, for its significant publications and heterogeneity among the included studies, the conclusion should be interpreted cautiously.

  14. Circulating adiponectin levels and risk of endometrial cancer: Systematic review and meta-analysis. (United States)

    Li, Zhi-Jun; Yang, Xue-Ling; Yao, Yan; Han, Wei-Qing; Li, B O


    Previous epidemiological studies have presented conflicting results regarding associations between circulating adiponectin (APN) levels and the risk of endometrial cancer. Thus a meta-analysis was performed to investigate the association between these factors. Multiple electronic sources, including PubMed, SpringerLink and Google Scholar databases were searched to identify relevant studies for the present meta-analysis. All of the selected studies examined the correlation between circulating APN levels and endometrial cancer. The standardized mean difference (SMD) and 95% confidence intervals (CIs) were estimated and pooled using meta-analysis methods. Overall, 18 case-control studies met the inclusion criteria. A total of 5,692 participants and 2,337 cases of endometrial cancer were included in this meta-analysis. The SMD of the pooled analysis (95% CI) were -1.96 (-2.60, -1.31), P=0.000. When the cancer grades were compared, the APN values were not significantly different between the grades of endometrial cancer [G1 vs. G3, 1.02 (-0.68, 2.72), P>0.05; G1 vs. G2, 0.34 (-0.86, 1.54), P>0.05]. However, there was a significant association between high APN levels and postmenopausal endometrial cancer cases with an SMD (95% CI) of -2.27 (-4.36, -0.18) and P0.05. The low circulating APN level increases the risk of endometrial cancer, whereas the high APN level decreases this risk in postmenopausal women. Circulating APN as simple biomarkers may be a promising tool for the prevention, early diagnosis and disease monitoring of endometrial cancer.

  15. Dietary intake and urinary level of cadmium and breast cancer risk: A meta-analysis. (United States)

    Lin, Jinbo; Zhang, Fang; Lei, Yixiong


    Cadmium, a human carcinogenic heavy metal, has been reported to be associated with breast cancer risk; however, the results from the epidemiological studies are not always consistent. The objective of this study was to quantitatively summarize the current evidence for the relationship between cadmium exposure and breast cancer risk using meta-analysis methods. Six studies determining the dietary cadmium intake level and five studies evaluating the urinary cadmium level were identified in a systematic search of MEDLINE and PubMed databases, and the associations between these levels and breast cancer risk were analysed. The pooled estimates under the random-effects model suggested that higher urinary cadmium levels were associated with an increased risk for breast cancer (highest versus lowest quantile, pooled odds ratio [OR]=2.24, 95% confidence interval [95%CI]=1.49-3.35) and a 1μg/g creatinine increase in urinary cadmium led to a 1.02-fold increment of breast cancer (pooled OR=2.02, 95%CI=1.34-3.03); however, pooled estimates for dietary cadmium intake found no significant association between cadmium exposure and breast cancer risk (highest versus lowest quantile, pooled relative risk [RR]=1.01, 95%CI=0.89-1.15). These results suggest that cadmium exposure may lead to an increased risk of breast cancer, and urinary cadmium levels can serve as a reliable biomarker for long-term cadmium exposure and may predict the breast cancer risk.

  16. The cost of cancer: a retrospective analysis of the financial impact of cancer on young adults. (United States)

    Landwehr, Michelle S; Watson, Samantha E; Macpherson, Catherine F; Novak, Katherine A; Johnson, Rebecca H


    Young adult cancer survivors (YAs) are confronted with immense financial challenges in the wake of their treatment. Medical bills and loss of savings may cause YAs to forgo recommended medications or follow-up appointments. Young survivors with financial concerns also report depression, stress and anxiety. The Samfund is a national nonprofit organization that provides financial support to YAs post-treatment. To quantify the financial burden of cancer in YAs, a retrospective analysis was performed of data collected from Samfund grant applications of 334 YA cancer survivors. Grants were awarded between 2007 and 2013 and grant recipients were consented electronically in 2014 for retrospective data analysis. Recipients ranged from 19 to 39 years of age at the time of their grant applications. Descriptive statistics were calculated and compared to the Medical Expenditure Panel Survey (MEPS) and U.S. census data on age-matched peers. Financial indicators of YA cancer survivors are worse in many domains than those of age-matched controls. Furthermore, YA survivors in their 30s report more perilous prefunding financial situations than younger grant recipients. Cancer has a devastating and age-specific impact on the finances of YAs. Philanthropic grants from the cancer support community, in conjunction with healthcare policy reforms, have the potential to break the cycle of financial need and help YAs move forward with their lives after cancer treatment.

  17. Model correction factor method for system analysis

    DEFF Research Database (Denmark)

    Ditlevsen, Ove Dalager; Johannesen, Johannes M.


    The Model Correction Factor Method is an intelligent response surface method based on simplifiedmodeling. MCFM is aimed for reliability analysis in case of a limit state defined by an elaborate model. Herein it isdemonstrated that the method is applicable for elaborate limit state surfaces on which...

  18. Matrix methods for bare resonator eigenvalue analysis. (United States)

    Latham, W P; Dente, G C


    Bare resonator eigenvalues have traditionally been calculated using Fox and Li iterative techniques or the Prony method presented by Siegman and Miller. A theoretical framework for bare resonator eigenvalue analysis is presented. Several new methods are given and compared with the Prony method.

  19. Secular trend analysis oflung cancer incidence inSihui city, China between1987 and 2011

    Institute of Scientific and Technical Information of China (English)

    JinLinDu; MingHuangHong; QiHongHuang; ZhengErLiao; SuMeiCao; XiaoLin; LiFangZhang; YanHuaLi; ShangHangXie; MengJieYang; JieGuo; ErHongLin; QingLiu


    Background:With industrial and economic development in recent decades in South China, cancer incidence may have changed due to the changing lifestyle and environment. However, the trends of lung cancer and the roles of smoking and other environmental risk factors in the development of lung cancer in rural areas of South China remain unclear. The purpose of this study was to explore the lung cancer incidence trends and the possible causes of these trends. Methods:Joinpoint regression analysis and the age–period–cohort (APC) model were used to analyze the lung can‑cer incidence trends in Sihui, Guangdong province, China between 1987 and 2011, and explore the possible causes of these trends. Results:A total of 2,397 lung cancer patients were involved in this study. A 3‑fold increase in the incidence of lung cancer in both sexes was observed over the 25‑year period. Joinpoint regression analysis showed that while the inci‑dence continued to increase steadily in females during the entire period, a sharp acceleration was observed in males starting in 2005. The full APC model was selected to describe age, period, and birth cohort effects on lung cancer inci‑dence trends in Sihui. The age cohorts in both sexes showed a continuously signiifcant increase in the relative risk (RR) of lung cancer, with a peak in the eldest age group (80–84years). The RR of lung cancer showed a lfuctuating curve in both sexes. The birth cohorts identiifed an increased trend in both males and females; however, males had a plateau in the youngest cohorts who were born during 1955–1969. Conclusions:Increasing trends of the incidence of lung cancer in Sihui were dominated by the effects of age and birth cohorts. Social aging, smoking, and environmental changes may play important roles in such trends.

  20. Comparative proteome analysis of human epithelial ovarian cancer

    Directory of Open Access Journals (Sweden)

    Gagné Jean-Philippe


    Full Text Available Abstract Background Epithelial ovarian cancer is a devastating disease associated with low survival prognosis mainly because of the lack of early detection markers and the asymptomatic nature of the cancer until late stage. Using two complementary proteomics approaches, a differential protein expression profile was carried out between low and highly transformed epithelial ovarian cancer cell lines which realistically mimic the phenotypic changes observed during evolution of a tumour metastasis. This investigation was aimed at a better understanding of the molecular mechanisms underlying differentiation, proliferation and neoplastic progression of ovarian cancer. Results The quantitative profiling of epithelial ovarian cancer model cell lines TOV-81D and TOV-112D generated using iTRAQ analysis and two-dimensional electrophoresis coupled to liquid chromatography tandem mass spectrometry revealed some proteins with altered expression levels. Several of these proteins have been the object of interest in cancer research but others were unrecognized as differentially expressed in a context of ovarian cancer. Among these, series of proteins involved in transcriptional activity, cellular metabolism, cell adhesion or motility and cytoskeleton organization were identified, suggesting their possible role in the emergence of oncogenic pathways leading to aggressive cellular behavior. Conclusion The differential protein expression profile generated by the two proteomics approaches combined to complementary characterizations studies will open the way to more exhaustive and systematic representation of the disease and will provide valuable information that may be helpful to uncover the molecular mechanisms related to epithelial ovarian cancer.

  1. Immunoexpression analysis and prognostic value of BLCAP in breast cancer.

    Directory of Open Access Journals (Sweden)

    Irina Gromova

    Full Text Available Bladder Cancer Associated Protein (BLCAP, formerly Bc10, was identified by our laboratory as being down-regulated in bladder cancer with progression. BLCAP is ubiquitously expressed in different tissues, and several studies have found differential expression of BLCAP in various cancer types, such as cervical and renal cancer, as well as human tongue carcinoma and osteosarcoma. Here we report the first study of the expression patterns of BLCAP in breast tissue. We analyzed by immunohistochemistry tissue sections of normal and malignant specimens collected from 123 clinical high-risk breast cancer patients within the Danish Center for Translational Breast Cancer Research (DCTB prospective study dataset. The staining pattern, the distribution of the immunostaining, and its intensity were studied in detail. We observed weak immunoreactivity for BLCAP in mammary epithelial cells, almost exclusively localizing to the cytoplasm and found that levels of expression of BLCAP were generally higher in malignant cells as compared to normal cells. Quantitative IHC analysis of BLCAP expression in breast tissues confirmed this differential BLCAP expression in tumor cells, and we could establish, in a 62-patient sample matched cohort, that immunostaining intensity for BLCAP was increased in tumors relative to normal tissue, in more than 45% of the cases examined, indicating that BLCAP may be of value as a marker for breast cancer. We also analyzed BLCAP expression and prognostic value using a set of tissue microarrays comprising an independent cohort of 2,197 breast cancer patients for which we had follow-up clinical information.

  2. Analysis of Mortality of Stomach Cancer in China from 1990-1992

    Institute of Scientific and Technical Information of China (English)

    XiudiSun; YaliZhang; LiandiLi; YoulinQiao


    OBJECTIVE To assess the impact of stom'ach cancer on the Chinese population by epidemiological analysis of its distributional mortality.METHODS Data from 1990-1992 on stomach cancer mortality collected by a sampling survey involved one tenth of the total Chinese population.RESULTS The crude mortality rate of stomach cancer in China was 25.2per 105 (32.8 per 105for males and 17.0 per 105 for females), which comprised23.2% of the total cancer deaths from 1990 to 1992, making stomach cancerthe leading cause of cancer death. The stomach cancer mortality rate ofmales was 1.9 times of that of females. The Chinese mortality rates ofstomach cancer adjusted by the world standard population were 40.8 per105 and 18.6 per 105 for males and females, which were 4.2-7.9 (for males)and 3.8-8.0 (for females) times of those in developed countries. Age-adjusted mortality rates of stomach cancer in China have distinctgeographical differences: form the lowest of 2.5 per 105 to the highest of153.0 per 105 in the 263 selected sites, and 15.3 per 105 in urban areas and24.4 per 105 in rural areas, a difference of 1.6 times.CONCW$10N The prevention and treatment of stomach cancer in L;n~na,especially in the countryside and the under-developed areas in thenorthwest, should be a long-term focus in preventing of cancers of thedigestive system. Urgent measures for prevention and early detection of stomach cancer should be taken.

  3. Self-care Concept Analysis in Cancer Patients: An Evolutionary Concept Analysis (United States)

    Hasanpour-Dehkordi, Ali


    Background: Self-care is a frequently used concept in both the theory and the clinical practice of nursing and is considered an element of nursing theory by Orem. The aim of this paper is to identify the core attributes of the self-care concept in cancer patients. Materials and Methods: We used Rodgers’ evolutionary method of concept analysis. The articles published in English language from 1980 to 2015 on nursing and non-nursing disciplines were analyzed. Finally, 85 articles, an MSc thesis, and a PhD thesis were selected, examined, and analyzed in-depth. Two experts checked the process of analysis and monitored and reviewed the articles. Results: The analysis showed that self-care concept is determined by four attributes of education, interaction, self-control, and self-reliance. Three types of antecedents in the present study were client-related (self-efficacy, self-esteem), system-related (adequate sources, social networks, and cultural factors), and healthcare professionals-related (participation). Conclusion: The self-care concept has considerably evolved among patients with chronic diseases, particularly cancer, over the past 35 years, and nurses have managed to enhance their knowledge about self-care remarkably for the clients so that the nurses in healthcare teams have become highly efficient and able to assume the responsibility for self-care teams. PMID:27803559

  4. Dietary cadmium intake and the risk of cancer: a meta-analysis.

    Directory of Open Access Journals (Sweden)

    Young Ae Cho

    Full Text Available BACKGROUND: Diet is a major source of cadmium intake among the non-smoking general population. Recent studies have determined that cadmium exposure may produce adverse health effects at lower exposure levels than previously predicted. We conducted a meta-analysis to combine and analyze the results of previous studies that have investigated the association of dietary cadmium intake and cancer risk. METHODS: We searched PubMed, EMBASE, and MEDLINE database for case-control and cohort studies that assessed the association of dietary cadmium intake and cancer risk. We performed a meta-analysis using eight eligible studies to summarize the data and summary relative risks (RRs and 95% confidence intervals (CIs were calculated using a random effects model. RESULTS: Overall, dietary cadmium intake showed no statistically significant association with cancer risk (RR = 1.10; 95% CI: 0.99-1.22, for highest vs. lowest dietary cadmium group. However, there was strong evidence of heterogeneity, and subgroup analyses were conducted using the study design, geographical location, and cancer type. In subgroup analyses, the positive associations between dietary cadmium intake and cancer risk were observed among studies with Western populations (RR = 1.15; 95% CI: 1.08-1.23 and studies investigating some hormone-related cancers (prostate, breast, and endometrial cancers. CONCLUSION: Our analysis found a positive association between dietary cadmium intake and cancer risk among studies conducted in Western countries, particularly with hormone-related cancers. Additional experimental and epidemiological studies are required to verify our findings.

  5. Diagnosis of breast cancer by tissue analysis

    Institute of Scientific and Technical Information of China (English)

    Debnath Bhattacharyya; Samir Kumar Bandyopadhyay; Tai-hoon Kim


    In this paper,we propose a technique to locate abnormal growth of cells in breast tissue and suggest further pathological test,when require.We compare normal breast tissue with malignant invasive breast tissue by a series of image processing steps.Normal ductal epithelial cells and ductal/lobular invasive carcinogenic cells also consider for comparison here in this paper.In fact,features of cancerous breast tissue (invasive) are extracted and analyses with normal breast tissue.We also suggest the breast cancer recognition technique through image processing and prevention by controlling p53 gene mutation to some extent.

  6. Retrospective analysis of cases with Endometrial Cancer

    Directory of Open Access Journals (Sweden)

    Bulat Aytek Şık


    Full Text Available We planned this study with the aim of determining histological types, clinical, surgical stage and grade of endometrial cancer cases which were followed-up and operated on in our clinic and giving an opinion on epidemiological features. Our study was a retrospective study consisted of 298 patients who had medical operations with the diagnosis of endometrial cancer. Endometrial cancer was diagnosed via dilatation and curettage. Routine preoperative examinations were wanted from the cases. Clinical stage was determined. After the diagnosis, total abdominal hysterectomy and bilateral salpingo-ooforectomy (TAH+BSO were applied; while only pelvic lymph node dissection was applied on the patients who had good prognostic data, total pelvic and paraaortic lymph node dissection were applied to the group with bad prognostic data. All materials were examined in the pathology laboratory of our hospital. In endometrial cancer staging, FIGO surgical staging system -2009 was used. FIGO was used in grade classification and World Health Organization Classification of Tumors system was used for the histological classification. Our study was composed of 298 patients who had endometrial cancer. Of the patients who were included in the study, average age was 56.54±9.69, BMI average was 31.47±6.20, gravida average was 4.16±2.59, and parity average was 3.41±2.15. Distributions of the patients by surgical stages were as follows; there were 32 patients whose tumor stage was in 1A (%10.7, 127 patients in 1B  (42.6%, 47 patients in 1C  (15.8%, 18 patients in 2A  (6.0%, 7 patients in 2B   (2.3%, 30 patients in 3A  (10.1%, 2 patients in 3B  (0.7%, 30 patients in 3C  (10.1%, 2 patients in 4A  (0.7% and 3 patients in 4B  (1.0%. Of the patients with endometrial cancer in our study, tumors of 102 patients were (34.2% in grade I, 139 were (46.6% in grade II and 57 were (19.1% in grade III. Because endometrial cancer shows earlier symptoms than the other

  7. Methods to Predict and Lower the Risk of Prostate Cancer

    Directory of Open Access Journals (Sweden)

    Barbara Ercole


    Full Text Available Chemoprevention for prostate cancer (PCa continues to generate interest from both physicians and the patient population. The goal of chemoprevention is to stop the malignant transformation of prostate cells into cancer. Multiple studies on different substances ranging from supplements to medical therapy have been undertaken. Thus far, only the studies on 5α-reductase inhibitors (the Prostate Cancer Prevention Trial [PCPT] and Reduction by Dutasteride of Prostate Cancer Events [REDUCE] trial have demonstrated a reduction in the risk of PCa, while results from the Selenium and Vitamin E Cancer Prevention Trial (SELECT concluded no decreased risk for PCa with selenium or vitamin E.

  8. Dairy products and colorectal cancer risk: a systematic review and meta-analysis of cohort studies.

    NARCIS (Netherlands)

    Aune, D.; Lau, R.; Chan, D.S.; Vieira, R.; Greenwood, D.C.; Kampman, E.; Norat, T.


    BACKGROUND: Previous studies of the association between intake of dairy products and colorectal cancer risk have indicated an inverse association with milk, however, the evidence for cheese or other dairy products is inconsistent. METHODS: We conducted a systematic review and meta-analysis to clarif

  9. Dairy products and colorectal cancer risk : a systematic review and meta-analysis of cohort studies

    NARCIS (Netherlands)

    Aune, D.; Lau, R.; Chan, D.S.M.; Vieira, R.; Greenwood, D.C.; Kampman, E.; Norat, T.


    Background: Previous studies of the association between intake of dairy products and colorectal cancer risk have indicated an inverse association with milk, however, the evidence for cheese or other dairy products is inconsistent. Methods: We conducted a systematic review and meta-analysis to clarif

  10. DD3(PCA3)-based molecular urine analysis for the diagnosis of prostate cancer.

    NARCIS (Netherlands)

    Hessels, D.; Klein Gunnewiek, J.M.T.; Oort, I.M. van; Karthaus, H.F.M.; Leenders, G.J.L.H. van; Balken, B. van; Kiemeney, L.A.L.M.; Witjes, J.A.; Schalken, J.A.


    BACKGROUND: DD3(PCA3) is the most prostate cancer-specific gene described to date. To assess the clinical utility of DD3(PCA3) a time-resolved fluorescence-based, quantitative RT-PCR analysis for DD3(PCA3) was developed. METHODS: The diagnostic potential of DD3(PCA3) was determined by quantitative

  11. Laparoscopic, robotic and open method of radical hysterectomy for cervical cancer: A systematic review

    Directory of Open Access Journals (Sweden)

    Puliyath Geetha


    Full Text Available Background : Over the last two decades, numerous studies have indicated the feasibility of minimally invasive surgery for early cervical cancer without compromising the oncological outcome. Objective : Systematic literature review and meta analysis aimed at evaluating the outcome of laparoscopic and robotic radical hysterectomy (LRH and RRH and comparing the results with abdominal radical hysterectomy (ARH. Search Strategy : Medline, PubMed, Embase, Cochrane library and Reference lists were searched for articles published until January 31 st 2011, using the terms radical hysterectomy, laparoscopic radical hysterectomy, robotic radical hysterectomy, surgical treatment of cervical cancer and complications of radical hysterectomy. Selection Criteria : Studies that reported outcome measures of radical hysterectomy by open method, laparoscopic and robotic methods were selected. Data collection and analysis: Two independent reviewers selected studies, abstracted and tabulated the data and pooled estimates were obtained on the surgical and oncological outcomes. Results : Mean sample size, age and body mass index across the three types of RH studies were similar. Mean operation time across the three types of RH studies was comparable. Mean blood loss and transfusion rate are significantly higher in ARH compared to both LRH and RRH. Duration of stay in hospital for RRH was significantly less than the other two methods. The mean number of lymph nodes obtained, nodal metastasis and positive margins across the three types of RH studies were similar. Post operative infectious morbidity was significantly higher among patients who underwent ARH compared to the other two methods and a higher rate of cystotomy in LRH. Conclusions : Minimally invasive surgery especially robotic radical hysterectomy may be a better and safe option for surgical treatment of cervical cancer. The laparoscopic method is not free from complications. However, experience of surgeon may

  12. Dietary Patterns and Pancreatic Cancer Risk: A Meta-Analysis. (United States)

    Lu, Pei-Ying; Shu, Long; Shen, Shan-Shan; Chen, Xu-Jiao; Zhang, Xiao-Yan


    A number of studies have examined the associations between dietary patterns and pancreatic cancer risk, but the findings have been inconclusive. Herein, we conducted this meta-analysis to assess the associations between dietary patterns and the risk of pancreatic cancer. MEDLINE (provided by the National Library of Medicine) and EBSCO (Elton B. Stephens Company) databases were searched for relevant articles published up to May 2016 that identified common dietary patterns. Thirty-two studies met the inclusion criteria and were finally included in this meta-analysis. A reduced risk of pancreatic cancer was shown for the highest compared with the lowest categories of healthy patterns (odds ratio, OR = 0.86; 95% confidence interval, CI: 0.77-0.95; p = 0.004) and light-moderate drinking patterns (OR = 0.90; 95% CI: 0.83-0.98; p = 0.02). There was evidence of an increased risk for pancreatic cancer in the highest compared with the lowest categories of western-type pattern (OR = 1.24; 95% CI: 1.06-1.45; p = 0.008) and heavy drinking pattern (OR = 1.29; 95% CI: 1.10-1.48; p = 0.002). The results of this meta-analysis demonstrate that healthy and light-moderate drinking patterns may decrease the risk of pancreatic cancer, whereas western-type and heavy drinking patterns may increase the risk of pancreatic cancer. Additional prospective studies are needed to confirm these findings.

  13. The correlation analysis of primary liver cancer with Type 2 diabetes

    Directory of Open Access Journals (Sweden)

    Q Su


    Full Text Available OBJECTIVE: To explore the relationship between Type 2 diabetes and primary liver cancer. MATERIALS AND METHODS: In the period from December 2008 to December 2014, all blood sugar data of patients in our hospital was collected, and the total number is 18213. Except for repeatedly hospitalized diabetic person, newborn stress status, or venous transfusion blood glucose, gestational diabetes, etc., By retrieving the medical record information of patients in the hospital, and using telephone or letter follow-up the patients, we collected 127 people with type 1 diabetes and found no liver cancer patients; Type 2 diabetes, 10,794 cases of patient information, 59 with primary liver cancer. For data analysis, Stata11.0 ratio was used as the main analysis indicators, using Chi-square test and statistical analysis. RESULTS: About 10,794 Type 2 diabetes cases with 59 primary liver cancer, the incidence is 54.66/10,000, men liver cancer incidence (92.78/10,000 than women (27.13/10,000, with significant difference (χ2 = 26.621, P < 0.001. As the growth of the age, the possibility of liver cancer in patients with diabetes increased significantly (χ2 = 19.961, P = 0.001. The rate was highest for 50-60-year-old men, and the women at age 70, and older incidence is highest. Irrespective of men or women with diabetes as the growth of the age, the possibility of liver cancer had significantly increased (P = 0.001, P = 0.002. Hepatitis B or hepatitis C incidence was 2.94%, but diabetes incidence of hepatitis men (3.98% and women (2.01% did not find significant differences (χ2 = 0.3361, P = 0.562. Three hundred and seventeen cases of Type 2 diabetes with hepatitis, the incidence of primary liver cancer was 11.67%, the liver cancer incidence of diabetes patients with hepatitis men (17.78% than women (3.97%, with significant difference (χ2 = 37.429, P < 0.001. With the growth of age, the overall risk of getting liver cancer (χ2 =15.023, P = 0.01 of diabetes and

  14. Beam-propagation method - Analysis and assessment (United States)

    van Roey, J.; van der Donk, J.; Lagasse, P. E.


    A method for the calculation of the propagation of a light beam through an inhomogeneous medium is presented. A theoretical analysis of this beam-propagation method is given, and a set of conditions necessary for the accurate application of the method is derived. The method is illustrated by the study of a number of integrated-optic structures, such as thin-film waveguides and gratings.

  15. Fractal methods in image analysis and coding


    Neary, David


    In this thesis we present an overview of image processing techniques which use fractal methods in some way. We show how these fields relate to each other, and examine various aspects of fractal methods in each area. The three principal fields of image processing and analysis th a t we examine are texture classification, image segmentation and image coding. In the area of texture classification, we examine fractal dimension estimators, comparing these methods to other methods in use, a...

  16. Menstrual Factors, Reproductive Factors 
and Lung Cancer Risk: A Meta-analysis

    Directory of Open Access Journals (Sweden)

    Yue ZHANG


    Full Text Available Background and objective Epidemiological studies have suggested that menstrual and reproductive factors may influence lung cancer risk, but the results are controversial. We therefore carried out a meta-analysis aiming to examine the associations of lung cancer in women with menstrual and reproductive factors. 
Methods Relevant studies were searched from PubMed database, CNKI, WANFANG DATA and VIP INFORMATION up to January 2012, with no language restrictions. References listed from selected papers were also reviewed. We included studies that reported the estimates of relative risks (RRs with 95% confidence intervals (CIs for the association between menstrual and reproductive factors and lung cancer risk. The pooled RRs were calculated after the heterogeneity test with the software Stata 11, and publication bias and sensitivity were evaluated at the same time. 
Results Twenty-five articles, representing 24 independent studies, were included in this meta-analysis. Older age at menarche in North America women (RR=0.83; 95%CI: 0.73-0.94 was associated with a significant decreased risk of lung cancer. Longer length of menstrual cycle was also associated with decreased lung cancer risk (RR=0.72; 95%CI: 0.57-0.90. Other exposures were not significantly associated. 
Conclusions Our analysis provides evidence of the hypothesis that female sex hormones influence the risk of lung cancer in women, yet additional studies are warranted to extend this finding and to clarify the underlying mechanisms.

  17. Research methods to change clinical practice for patients with rare cancers. (United States)

    Billingham, Lucinda; Malottki, Kinga; Steven, Neil


    Rare cancers are a growing group as a result of reclassification of common cancers by molecular markers. There is therefore an increasing need to identify methods to assess interventions that are sufficiently robust to potentially affect clinical practice in this setting. Methods advocated for clinical trials in rare diseases are not necessarily applicable in rare cancers. This Series paper describes research methods that are relevant for rare cancers in relation to the range of incidence levels. Strategies that maximise recruitment, minimise sample size, or maximise the usefulness of the evidence could enable the application of conventional clinical trial design to rare cancer populations. Alternative designs that address specific challenges for rare cancers with the aim of potentially changing clinical practice include Bayesian designs, uncontrolled n-of-1 trials, and umbrella and basket trials. Pragmatic solutions must be sought to enable some level of evidence-based health care for patients with rare cancers.

  18. Cancer Reporting: Timeliness Analysis and Process Reengineering (United States)

    Jabour, Abdulrahman M.


    Introduction: Cancer registries collect tumor-related data to monitor incident rates and support population-based research. A common concern with using population-based registry data for research is reporting timeliness. Data timeliness have been recognized as an important data characteristic by both the Centers for Disease Control and Prevention…

  19. ANOVA like analysis of cancer death age (United States)

    Areia, Aníbal; Mexia, João T.


    We use ANOVA to study the influence of year, sex, country and location on the average cancer death age. The data used was from the World Health Organization (WHO) files for 1999, 2003, 2007 and 2011. The locations considered were: kidney, leukaemia, melanoma of skin and oesophagus and the countries: Portugal, Norway, Greece and Romania.

  20. Dietary acrylamide and cancer risk: an updated meta-analysis. (United States)

    Pelucchi, Claudio; Bosetti, Cristina; Galeone, Carlotta; La Vecchia, Carlo


    The debate on the potential carcinogenic effect of dietary acrylamide is open. In consideration of the recent findings from large prospective investigations, we conducted an updated meta-analysis on acrylamide intake and the risk of cancer at several sites. Up to July 2014, we identified 32 publications. We performed meta-analyses to calculate the summary relative risk (RR) of each cancer site for the highest versus lowest level of intake and for an increment of 10 µg/day of dietary acrylamide, through fixed-effects or random-effects models, depending on the heterogeneity test. Fourteen cancer sites could be examined. No meaningful associations were found for most cancers considered. The summary RRs for high versus low acrylamide intake were 0.87 for oral and pharyngeal, 1.14 for esophageal, 1.03 for stomach, 0.94 for colorectal, 0.93 for pancreatic, 1.10 for laryngeal, 0.88 for lung, 0.96 for breast, 1.06 for endometrial, 1.12 for ovarian, 1.00 for prostate, 0.93 for bladder and 1.13 for lymphoid malignancies. The RR was of borderline significance only for kidney cancer (RR = 1.20; 95% confidence interval, CI, 1.00-1.45). All the corresponding continuous estimates ranged between 0.95 and 1.03, and none of them was significant. Among never-smokers, borderline associations with dietary acrylamide emerged for endometrial (RR = 1.23; 95% CI, 1.00-1.51) and ovarian (RR = 1.39; 95% CI, 0.97-2.00) cancers. This systematic review and meta-analysis of epidemiological studies indicates that dietary acrylamide is not related to the risk of most common cancers. A modest association for kidney cancer, and for endometrial and ovarian cancers in never smokers only, cannot be excluded.

  1. Spatial Analysis of Stomach Cancer Incidence in Iran. (United States)

    Pakzad, Reza; Khani, Yousef; Pakzad, Iraj; Momenimovahed, Zohre; Mohammadian-Hashejani, Abdollah; Salehiniya, Hamid; Towhidi, Farhad; Makhsosi, Behnam Reza


    Stomach cancer, the fourth most common cancer and the second leading cause of cancer-related death through the world, is very common in parts of Iran. Geographic variation in the incidence of stomach cancer is due to many different factors. The aim of this study was to assess the geographical and spatial distribution of stomach cancer in Iran using data from the cancer registry program in Iran for the year 2009. The reported incidences of stomach cancer for different provinces were standardized to the world population structure. ArcGIS software was used to analyse the data. Hot spots and high risk areas were determined using spatial analysis (Getis-Ord Gi). Hot and cold spots were determined as more than or less than 2 standard deviations from the national average, respectively. A significance level of 0.10 was used for statistical judgment. In 2009, a total of 6,886 cases of stomach cancers were reported of which 4,891 were in men and 1,995 in women (standardized incidence rates of 19.2 and 10.0, respectively, per 100,000 population). The results showed that stomach cancer was concentrated mainly in northwest of the country in both men and women. In women, northwest provinces such as Ardebil, East Azerbaijan, West Azerbaijan, Gilan, and Qazvin were identified as hot spots (pQazvin, Zanjan and Kurdistan, the incidences were higher than the national average and these were identified as hot spots (P<0.01). As stomach cancer is clustered in the northwest of the country, further epidemiological studies are needed to identify factors contributing to this concentration.



    Fedoseeva O. S.


    The article proposes a method for landscape area analysis, which consists of four stages. Technique is proposed as a tool for the practical application of pre-project research materials in the design solutions for landscape areas planning and organization

  3. An introduction to numerical methods and analysis

    CERN Document Server

    Epperson, James F


    Praise for the First Edition "". . . outstandingly appealing with regard to its style, contents, considerations of requirements of practice, choice of examples, and exercises.""-Zentralblatt MATH "". . . carefully structured with many detailed worked examples.""-The Mathematical Gazette The Second Edition of the highly regarded An Introduction to Numerical Methods and Analysis provides a fully revised guide to numerical approximation. The book continues to be accessible and expertly guides readers through the many available techniques of numerical methods and analysis. An Introduction to

  4. [Framework analysis method in qualitative research]. (United States)

    Liao, Xing; Liu, Jian-ping; Robison, Nicola; Xie, Ya-ming


    In recent years a number of qualitative research methods have gained popularity within the health care arena. Despite this popularity, different qualitative analysis methods pose many challenges to most researchers. The present paper responds to the needs expressed by recent Chinese medicine researches. The present paper is mainly focused on the concepts, nature, application of framework analysis, especially on how to use it, in such a way to assist the newcomer of Chinese medicine researchers to engage with the methodology.

  5. Magnetic resonance elastography (MRE) in cancer: Technique, analysis, and applications (United States)

    Pepin, Kay M.; Ehman, Richard L.; McGee, Kiaran P.


    Tissue mechanical properties are significantly altered with the development of cancer. Magnetic resonance elastography (MRE) is a noninvasive technique capable of quantifying tissue mechanical properties in vivo. This review describes the basic principles of MRE and introduces some of the many promising MRE methods that have been developed for the detection and characterization of cancer, evaluation of response to therapy, and investigation of the underlying mechanical mechanisms associated with malignancy. PMID:26592944

  6. Selenium Exposure and Cancer Risk: an Updated Meta-analysis and Meta-regression. (United States)

    Cai, Xianlei; Wang, Chen; Yu, Wanqi; Fan, Wenjie; Wang, Shan; Shen, Ning; Wu, Pengcheng; Li, Xiuyang; Wang, Fudi


    The objective of this study was to investigate the associations between selenium exposure and cancer risk. We identified 69 studies and applied meta-analysis, meta-regression and dose-response analysis to obtain available evidence. The results indicated that high selenium exposure had a protective effect on cancer risk (pooled OR = 0.78; 95%CI: 0.73-0.83). The results of linear and nonlinear dose-response analysis indicated that high serum/plasma selenium and toenail selenium had the efficacy on cancer prevention. However, we did not find a protective efficacy of selenium supplement. High selenium exposure may have different effects on specific types of cancer. It decreased the risk of breast cancer, lung cancer, esophageal cancer, gastric cancer, and prostate cancer, but it was not associated with colorectal cancer, bladder cancer, and skin cancer.

  7. Two MIS Analysis Methods: An Experimental Comparison. (United States)

    Wang, Shouhong


    In China, 24 undergraduate business students applied data flow diagrams (DFD) to a mini-case, and 20 used object-oriented analysis (OOA). DFD seemed easier to learn, but after training, those using the OOA method for systems analysis made fewer errors. (SK)

  8. An Analysis Method of Business Application Framework

    Institute of Scientific and Technical Information of China (English)


    We discuss the evolution of object-oriented software developmentpr o cess based on software pattern. For developing mature software fra mework and component, we advocate to elicit and incorporate software patterns fo r ensuing quality and reusability of software frameworks. On the analysis base o f requirement specification for business application domain, we present analysis method and basic role model of software framework. We also elicit analysis patt ern of framework architecture, and design basic role classes and their structure .

  9. Feasibility of breast cancer screening by PIXE analysis of hair. (United States)

    Gholizadeh, N; Kabiri, Z; Kakuee, O; Saleh-Kotahi, M; Changizi, V; Fathollahi, V; Oliaiy, P; Omranipour, R


    To reveal the role of key elements present in the hair of breast cancer patients on cancer development, the levels of a number of elements in scalp hair samples of 82 people including healthy individuals, people suffering from benign breast disease, and breast cancer patients were measured by PIXE analysis. Pellets of hair samples were prepared and bombarded by 2.2 MeV proton beam of a 3-MV Van de Graaff accelerator. The number of incident ions hitting the sample was indirectly measured using the RBS spectrum of a thin Ag film placed in the beam path. The concentrations of S, Cl, K, Ca, Fe, and Cu in the hair of healthy individuals were in agreement with those observed in the hair of hyperplasia and cancer patients within standard deviations. However, a lower average level of zinc was found in samples from hyperplasia and breast cancer patients. Strong positive correlations were found between iron and potassium as well as between calcium and potassium in the cancer patients. These results could be of significance in the screening for breast cancer.

  10. Proteomics Analysis for Finding Serum Markers of Ovarian Cancer

    Directory of Open Access Journals (Sweden)

    Yushan Cheng


    Full Text Available A combination of peptide ligand library beads (PLLB and 1D gel liquid chromatography-mass spectrometry/mass spectrometry (1DGel-LC-MS/MS was employed to analyze serum samples from patients with ovarian cancer and from healthy controls. Proteomic analysis identified 1200 serum proteins, among which 57 proteins were upregulated and 10 were downregulated in the sera from cancer patients. Retinol binding protein 4 (RBP4 is highly upregulated in the ovarian cancer serum samples. ELISA was employed to measure plasma concentrations of RBP4 in 80 samples from ovarian cancer patients, healthy individuals, myoma patients, and patients with benign ovarian tumor, respectively. The plasma concentrations of RBP4 ranging from 76.91 to 120.08 ng/mL with the mean value 89.13±1.67 ng/mL in ovarian cancer patients are significantly higher than those in healthy individuals (10.85±2.38 ng/mL. Results were further confirmed with immunohistochemistry, demonstrating that RBP4 expression levels in normal ovarian tissue were lower than those in ovarian cancer tissues. Our results suggested that RBP4 is a potential biomarker for diagnostic of screening ovarian cancer.

  11. LC-MS/MS Analysis Unravels Deep Oxidation of Manganese Superoxide Dismutase in Kidney Cancer (United States)

    Zhao, Zuohui; Azadzoi, Kazem M.; Choi, Han-Pil; Jing, Ruirui; Lu, Xin; Li, Cuiling; Wang, Fengqin; Lu, Jiaju; Yang, Jing-Hua


    Manganese superoxide dismutase (MNSOD) is one of the major scavengers of reactive oxygen species (ROS) in mitochondria with pivotal regulatory role in ischemic disorders, inflammation and cancer. Here we report oxidative modification of MNSOD in human renal cell carcinoma (RCC) by the shotgun method using data-dependent liquid chromatography tandem mass spectrometry (LC-MS/MS). While 5816 and 5571 proteins were identified in cancer and adjacent tissues, respectively, 208 proteins were found to be up- or down-regulated (p kidney cancer due to modifications. Thus, LC-MS/MS analysis revealed multiple oxidative modifications of MNSOD at different amino acid residues that might mediate the regulation of the superoxide radicals, mitochondrial ROS scavenging and MNSOD activity in kidney cancer. PMID:28165386

  12. Gastric Cancer Risk Analysis in Unhealthy Habits Data with Classification Algorithms

    Directory of Open Access Journals (Sweden)

    Kirshners Arnis


    Full Text Available Data mining methods are applied to a medical task that seeks for the information about the influence of Helicobacter Pylori on the gastric cancer risk increase by analysing the adverse factors of individual lifestyle. In the process of data preprocessing, the data are cleared of noise and other factors, reduced in dimensionality, as well as transformed for the task and cleared of non-informative attributes. Data classification using C4.5, CN2 and k-nearest neighbour algorithms is carried out to find relationships between the analysed attributes and the descriptive class attribute – Helicobacter Pylori presence that could have influence on the cancer development risk. Experimental analysis is carried out using the data of the Latvian-based project “Interdisciplinary Research Group for Early Cancer Detection and Cancer Prevention” database.

  13. Combination of retrograde superselective intra-arterial chemotherapy and Seldinger method in locally advanced oral cancer

    Directory of Open Access Journals (Sweden)

    Masataka Uehara


    Full Text Available The nonsurgical strategies for locally advanced oral cancer are desirable. Superselective intra-arterial infusion with radiotherapy was utilized for this purpose, and there are two types of superselective intra-arterial infusion methods: The Seldinger method and the retrograde superselective intra-arterial chemotherapy (HFT method. In one case, the HFT method was applied to locally advanced tongue cancer, and the Seldinger method was used for additional administration of cisplatin (CDDP to compensate for a lack of drug flow in the HFT method. In another case, the HFT method was applied to locally advanced lower gingival cancer. The Seldinger method was applied to metastatic lymph nodes. In both cases, additional administration of CDDP using the Seldinger method resulted in a complete response. The combination of the HFT and Seldinger methods was useful to eradicate locally advanced oral cancer because each method compensated for the defects of the other.

  14. Combination of retrograde superselective intra-arterial chemotherapy and Seldinger method in locally advanced oral cancer. (United States)

    Uehara, Masataka; Ohya, Ryouichi; Kodama, Masaaki; Shiraishi, Takeshi; Asahina, Izumi; Tominaga, Kazuhiro


    The nonsurgical strategies for locally advanced oral cancer are desirable. Superselective intra-arterial infusion with radiotherapy was utilized for this purpose, and there are two types of superselective intra-arterial infusion methods: The Seldinger method and the retrograde superselective intra-arterial chemotherapy (HFT method). In one case, the HFT method was applied to locally advanced tongue cancer, and the Seldinger method was used for additional administration of cisplatin (CDDP) to compensate for a lack of drug flow in the HFT method. In another case, the HFT method was applied to locally advanced lower gingival cancer. The Seldinger method was applied to metastatic lymph nodes. In both cases, additional administration of CDDP using the Seldinger method resulted in a complete response. The combination of the HFT and Seldinger methods was useful to eradicate locally advanced oral cancer because each method compensated for the defects of the other.

  15. Evaluation of algorithm methods for fluorescence spectra of cancerous and normal human tissues (United States)

    Pu, Yang; Wang, Wubao; Alfano, Robert R.


    The paper focus on the various algorithms on to unravel the fluorescence spectra by unmixing methods to identify cancerous and normal human tissues from the measured fluorescence spectroscopy. The biochemical or morphologic changes that cause fluorescence spectra variations would appear earlier than the histological approach; therefore, fluorescence spectroscopy holds a great promise as clinical tool for diagnosing early stage of carcinomas and other deceases for in vivo use. The method can further identify tissue biomarkers by decomposing the spectral contributions of different fluorescent molecules of interest. In this work, we investigate the performance of blind source un-mixing methods (backward model) and spectral fitting approaches (forward model) in decomposing the contributions of key fluorescent molecules from the tissue mixture background when certain selected excitation wavelength is applied. Pairs of adenocarcinoma as well as normal tissues confirmed by pathologist were excited by selective wavelength of 340 nm. The emission spectra of resected fresh tissue were used to evaluate the relative changes of collagen, reduced nicotinamide adenine dinucleotide (NADH), and Flavin by various spectral un-mixing methods. Two categories of algorithms: forward methods and Blind Source Separation [such as Principal Component Analysis (PCA) and Independent Component Analysis (ICA), and Nonnegative Matrix Factorization (NMF)] will be introduced and evaluated. The purpose of the spectral analysis is to discard the redundant information which conceals the difference between these two types of tissues, but keep their diagnostically significance. The facts predicted by different methods were compared to the gold standard of histopathology. The results indicate that these key fluorophores within tissue, e.g. tryptophan, collagen, and NADH, and flavin, show differences of relative contents of fluorophores among different types of human cancer and normal tissues. The

  16. Nanoparticle therapeutics: Technologies and methods for overcoming cancer. (United States)

    Cerqueira, Brenda Brenner S; Lasham, Annette; Shelling, Andrew N; Al-Kassas, Raida


    It is anticipated that by 2030 approximately 13 million people will die of cancer. Common cancer therapy often fails due to the development of multidrug resistance (MDR), resulting in high morbidity and poor patient prognosis. Nanotechnology seeks to use drug delivery vehicles of 1-100 nm in diameter, made up of several different materials to deliver anti-cancer drugs selectively to cancer cells and potentially overcome MDR. Several technologies exist for manufacturing and functionalizing nanoparticles. When functionalized appropriately, nanoparticles have been shown to overcome several mechanisms of MDR in vivo and in vitro, reduce drug side effects and represent a promising new area of anti-cancer therapy. This review discusses the fundamental concepts of enhanced permeability and retention (EPR) effect and explores the mechanisms proposed to enhance preferential "retention" in the tumour. The overall objective of this review was to enhance our understanding in the design and development of therapeutic nanoparticles for treatment of cancer.

  17. Impact of socioeconomic inequalities on geographic disparities in cancer incidence: comparison of methods for spatial disease mapping

    Directory of Open Access Journals (Sweden)

    Juste Aristide Goungounga


    Full Text Available Abstract Background The reliability of spatial statistics is often put into question because real spatial variations may not be found, especially in heterogeneous areas. Our objective was to compare empirically different cluster detection methods. We assessed their ability to find spatial clusters of cancer cases and evaluated the impact of the socioeconomic status (e.g., the Townsend index on cancer incidence. Methods Moran’s I, the empirical Bayes index (EBI, and Potthoff-Whittinghill test were used to investigate the general clustering. The local cluster detection methods were: i the spatial oblique decision tree (SpODT; ii the spatial scan statistic of Kulldorff (SaTScan; and, iii the hierarchical Bayesian spatial modeling (HBSM in a univariate and multivariate setting. These methods were used with and without introducing the Townsend index of socioeconomic deprivation known to be related to the distribution of cancer incidence. Incidence data stemmed from the Cancer Registry of Isère and were limited to prostate, lung, colon-rectum, and bladder cancers diagnosed between 1999 and 2007 in men only. Results The study found a spatial heterogeneity (p 1.2. The multivariate HBSM found a spatial correlation between lung and bladder cancers (r = 0.6. Conclusions In spatial analysis of cancer incidence, SpODT and HBSM may be used not only for cluster detection but also for searching for confounding or etiological factors in small areas. Moreover, the multivariate HBSM offers a flexible and meaningful modeling of spatial variations; it shows plausible previously unknown associations between various cancers.

  18. A Review of Current Machine Learning Methods Used for Cancer Recurrence Modeling and Prediction

    Energy Technology Data Exchange (ETDEWEB)

    Hemphill, Geralyn M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)


    Cancer has been characterized as a heterogeneous disease consisting of many different subtypes. The early diagnosis and prognosis of a cancer type has become a necessity in cancer research. A major challenge in cancer management is the classification of patients into appropriate risk groups for better treatment and follow-up. Such risk assessment is critically important in order to optimize the patient’s health and the use of medical resources, as well as to avoid cancer recurrence. This paper focuses on the application of machine learning methods for predicting the likelihood of a recurrence of cancer. It is not meant to be an extensive review of the literature on the subject of machine learning techniques for cancer recurrence modeling. Other recent papers have performed such a review, and I will rely heavily on the results and outcomes from these papers. The electronic databases that were used for this review include PubMed, Google, and Google Scholar. Query terms used include “cancer recurrence modeling”, “cancer recurrence and machine learning”, “cancer recurrence modeling and machine learning”, and “machine learning for cancer recurrence and prediction”. The most recent and most applicable papers to the topic of this review have been included in the references. It also includes a list of modeling and classification methods to predict cancer recurrence.

  19. Clinicopathological characteristics and prognostic value of cancer stem cell marker CD133 in breast cancer: a meta-analysis (United States)

    Li, Zhan; Yin, Songcheng; Zhang, Lei; Liu, Weiguang; Chen, Bo; Xing, Hua


    Background The association of CD133 overexpression with clinicopathological significance and prognosis in patients with breast cancer remains controversial. We thus performed a meta-analysis to evaluate the role of CD133 expression in the development and prognosis of breast cancer. Methods The databases PubMed, Embase, and Cochrane Library (updated to August 1, 2016) were searched. Pooled odds ratios (ORs) or hazard ratios (HRs) with 95% confidence intervals (95% CI) were used to evaluate the impact of CD133 expression on clinicopathological features, overall survival, and disease-free survival. Results A total of 1,734 patients from 13 studies were subject to final analysis. The results showed a significant association between overexpression of CD133 and estrogen receptor status (OR 0.35, 95% CI 0.18–0.70), progesterone receptor status (OR 0.56, 95% CI 0.43–0.74), human epidermal growth factor-2 status (OR 1.81, 95% CI 1.33–2.45), lymph node metastasis (OR 1.98, 95% CI 1.34–2.92), and tumor histological grade (OR 1.79, 95% CI 1.26–2.54) in breast cancer. However, no significant correlation was found between upregulation of CD133 expression and onset age (OR 1.03, 95% CI 0.70–1.53) or tumor size (OR 1.29, 95% CI 0.80–2.09). Moreover, CD133-positive breast cancer patients had a higher risk of mortality (HR 1.91, 95% CI 1.21–3.03) and disease progression (HR 2.70, 95% CI 1.05–6.95). Conclusion This meta-analysis suggested that CD133 might be a predictor of clinical outcomes as well as prognosis and could be a potentially new gene therapy target for breast cancer patients.

  20. Causal Moderation Analysis Using Propensity Score Methods (United States)

    Dong, Nianbo


    This paper is based on previous studies in applying propensity score methods to study multiple treatment variables to examine the causal moderator effect. The propensity score methods will be demonstrated in a case study to examine the causal moderator effect, where the moderators are categorical and continuous variables. Moderation analysis is an…

  1. Error Analysis of Band Matrix Method


    Taniguchi, Takeo; Soga, Akira


    Numerical error in the solution of the band matrix method based on the elimination method in single precision is investigated theoretically and experimentally, and the behaviour of the truncation error and the roundoff error is clarified. Some important suggestions for the useful application of the band solver are proposed by using the results of above error analysis.

  2. Relating Actor Analysis Methods to Policy Problems

    NARCIS (Netherlands)

    Van der Lei, T.E.


    For a policy analyst the policy problem is the starting point for the policy analysis process. During this process the policy analyst structures the policy problem and makes a choice for an appropriate set of methods or techniques to analyze the problem (Goeller 1984). The methods of the policy anal

  3. Empirical likelihood method in survival analysis

    CERN Document Server

    Zhou, Mai


    Add the Empirical Likelihood to Your Nonparametric ToolboxEmpirical Likelihood Method in Survival Analysis explains how to use the empirical likelihood method for right censored survival data. The author uses R for calculating empirical likelihood and includes many worked out examples with the associated R code. The datasets and code are available for download on his website and CRAN.The book focuses on all the standard survival analysis topics treated with empirical likelihood, including hazard functions, cumulative distribution functions, analysis of the Cox model, and computation of empiric

  4. The feeling of hope in cancer patients: an existential analysis

    Directory of Open Access Journals (Sweden)

    Catarina Aparecida Sales


    Full Text Available This study aimed at unveiling the feeling of hope in people who experience cancer in their existence. Qualitative study based on Heidegger’s phenomenology, performed with eight cancer patients assisted in a philanthropic organization, between December 2013 and February 2014, in a northwestern city in Paraná, Brazil, using the following guiding question: “How do you perceive the feeling of hope at this time in your life?” The analysis resulted in the ontological themes: searching for hope in dealing with cancer, and experiencing feelings of hope and despair in being with others. Patients revealed mixed feelings, going from the lack of hope at the time of diagnosis to a rekindling of hope, as well as those who never lost the will to live. We conclude that living with cancer causes extreme feelings; and hope emerges as a feeling capable of influencing and causes an expressive impact in coping with that.

  5. A New Immunologic Method for Detection of Occult Breast Cancer (United States)


    215, 1988. 29 P.I., Rishab K. Gupta, Ph.D. 38. Repetto L, Onetto M, Gardin G, Costanzi B, Guidici S, Vitiello E, Merlini L, Naso C, Zannini C...Serum CA15-3 assay in the diagnosis and follow-up of breast cancer. BrJ Cancer 58: 213-215, 1988. 40. Repetto L, Onetto M, Gardin G, Costanzi B... REPETTO L, ONETTO M, GARDIN G, et al: Serum CEA, CA15-3, and MCA in breast cancer patients: A clinical evaluation. Cancer Detection & Prevention 17:411

  6. Integrated genomic analysis of breast cancers. (United States)

    Addou-Klouche, L; Adélaïde, J; Cornen, S; Bekhouche, I; Finetti, P; Guille, A; Sircoulomb, F; Raynaud, S; Bertucci, F; Birnbaum, D; Chaffanet, M


    Breast cancer is the most frequent and the most deadly cancer in women in Western countries. Different classifications of disease (anatomoclinical, pathological, prognostic, genetic) are used for guiding the management of patients. Unfortunately, they fail to reflect the whole clinical heterogeneity of the disease. Consequently, molecularly distinct diseases are grouped in similar clinical classes, likely explaining the different clinical outcome between patients in a given class, and the fact that selection of the most appropriate diagnostic or therapeutic strategy for each patient is not done accurately. Today, treatment is efficient in only 70.0-75.0% of cases overall. Our repertoire of efficient drugs is limited but is being expanded with the discovery of new molecular targets for new drugs, based on the identification of candidate oncogenes and tumor suppressor genes (TSG) functionally relevant in disease. Development of new drugs makes therapeutical decisions even more demanding of reliable classifiers and prognostic/predictive tests. Breast cancer is a complex, heterogeneous disease at the molecular level. The combinatorial molecular origin and the heterogeneity of malignant cells, and the variability of the host background, create distinct subgroups of tumors endowed with different phenotypic features such as response to therapy and clinical outcome. Cellular and molecular analyses can identify new classes biologically and clinically relevant, as well as provide new clinically relevant markers and targets. The various stages of mammary tumorigenesis are not clearly defined and the genetic and epigenetic events critical to the development and aggressiveness of breast cancer are not precisely known. Because the phenotype of tumors is dependent on many genes, a large-scale and integrated molecular characterization of the genetic and epigenetic alterations and gene expression deregulation should allow the identification of new molecular classes clinically

  7. Representation of cancer in the medical literature--a bibliometric analysis.

    Directory of Open Access Journals (Sweden)

    Ronan W Glynn

    Full Text Available BACKGROUND: There exists a lack of knowledge regarding the quantity and quality of scientific yield in relation to individual cancer types. We aimed to measure the proportion, quality and relevance of oncology-related articles, and to relate this output to their associated disease burden. By incorporating the impact factor(IF and Eigenfactor™(EF into our analysis we also assessed the relationship between these indices and the output under study. METHODS: All publications in 2007 were retrieved for the 26 most common cancers. The top 20 journals ranked by IF and EF in general medicine and oncology, and the presence of each malignancy within these titles was analysed. Journals publishing most prolifically on each cancer were identified and their impact assessed. PRINCIPAL FINDINGS: 63260 (PubMed and 126845 (WoS entries were generated, respectively. 26 neoplasms accounted for 25% of total output from the top medical publications. 5 cancers dominated the first quartile of output in the top oncology journals; breast, prostate, lung, and intestinal cancer, and leukaemia. Journals associated with these cancers were associated with much higher IFs and EFs than those journals associated with the other cancer types under study, although these measures were not equivalent across all sub-specialties. In addition, yield on each cancer was related to its disease burden as measured by its incidence and prevalence. CONCLUSIONS: Oncology enjoys disproportionate representation in the more prestigious medical journals. 5 cancers dominate yield, although this attention is justified given their associated disease burden. The commonly used IF and the recently introduced EF do not correlate in the assessment of the preeminent oncology journals, nor at the level of individual malignancies; there is a need to delineate between proxy measures of quality and the relevance of output when assessing its merit. These results raise significant questions regarding the best

  8. Urban sprawl, obesity, and cancer mortality in the United States: cross-sectional analysis and methodological challenges


    Berrigan, David; Tatalovich, Zaria; Pickle, Linda W; Ewing, Reid; Ballard-Barbash, Rachel


    Background Urban sprawl has the potential to influence cancer mortality via direct and indirect effects on obesity, access to health services, physical activity, transportation choices and other correlates of sprawl and urbanization. Methods This paper presents a cross-sectional analysis of associations between urban sprawl and cancer mortality in urban and suburban counties of the United States. This ecological analysis was designed to examine whether urban sprawl is associated with total an...

  9. Health seeking behavioral analysis associated with breast cancer screening among Asian American women

    Directory of Open Access Journals (Sweden)

    Ma GX


    Full Text Available Grace X Ma,1 Wanzhen Gao,1 Sunmin Lee,2 MinQi Wang,3 Yin Tan,1 Steven E Shive,1,41Department of Public Health, Center for Asian Health, College of Health Professions, Temple University, Philadelphia, PA, USA; 2Department of Epidemiology and Biostatistics, School of Public Health, University of Maryland, College Park, MD, USA; 3Department of Public and Community Health, University of Maryland, College Park, Maryland, MD, USA; 4East Stroudsburg University, East Stroudsburg, PA, USAObjective: The purpose of this community-based study was to apply a Sociocultural Health Behavior Model to determine the association of factors proposed in the model with breast cancer screening behaviors among Asian American women.Methods: A cross-sectional design included a sample of 682 Chinese, Korean, and Vietnamese women aged 40 years and older. The frequency distribution analysis and Chi-square analysis were used for the initial screening of the following variables: sociodemographic, cultural, enabling, environmental, and social support. Univariate and multivariate analyses were conducted on factors for breast cancer screening using multinomial logistic regression analysis.Results: Correlates to positive breast cancer screening included demographics (ethnicity, cultural factors (living in the United States for 15 years or more, speaking English well, enabling factors (having a regular physician to visit, health insurance covering the screening, and family/social support factors (those who had a family/friend receiving a mammogram.Conclusions: The results of this study suggest that breast cancer screening programs will be more effective if they include the cultural and health beliefs, enabling, and social support factors associated with breast cancer screening. The use of community organizations may play a role in helping to increase breast cancer screening rates among Asian American women.Keywords: breast cancer screening, Vietnamese, Korean, Chinese, breast

  10. Elucidating the altered transcriptional programs in breast cancer using independent component analysis.

    Directory of Open Access Journals (Sweden)

    Andrew E Teschendorff


    Full Text Available The quantity of mRNA transcripts in a cell is determined by a complex interplay of cooperative and counteracting biological processes. Independent Component Analysis (ICA is one of a few number of unsupervised algorithms that have been applied to microarray gene expression data in an attempt to understand phenotype differences in terms of changes in the activation/inhibition patterns of biological pathways. While the ICA model has been shown to outperform other linear representations of the data such as Principal Components Analysis (PCA, a validation using explicit pathway and regulatory element information has not yet been performed. We apply a range of popular ICA algorithms to six of the largest microarray cancer datasets and use pathway-knowledge and regulatory-element databases for validation. We show that ICA outperforms PCA and clustering-based methods in that ICA components map closer to known cancer-related pathways, regulatory modules, and cancer phenotypes. Furthermore, we identify cancer signalling and oncogenic pathways and regulatory modules that play a prominent role in breast cancer and relate the differential activation patterns of these to breast cancer phenotypes. Importantly, we find novel associations linking immune response and epithelial-mesenchymal transition pathways with estrogen receptor status and histological grade, respectively. In addition, we find associations linking the activity levels of biological pathways and transcription factors (NF1 and NFAT with clinical outcome in breast cancer. ICA provides a framework for a more biologically relevant interpretation of genomewide transcriptomic data. Adopting ICA as the analysis tool of choice will help understand the phenotype-pathway relationship and thus help elucidate the molecular taxonomy of heterogeneous cancers and of other complex genetic diseases.

  11. Insights into pancreatic cancer etiology from pathway analysis of genome-wide association study data.

    Directory of Open Access Journals (Sweden)

    Peng Wei

    Full Text Available Pancreatic cancer is the fourth leading cause of cancer death in the U.S. and the etiology of this highly lethal disease has not been well defined. To identify genetic susceptibility factors for pancreatic cancer, we conducted pathway analysis of genome-wide association study (GWAS data in 3,141 pancreatic cancer patients and 3,367 controls with European ancestry.Using the gene set ridge regression in association studies (GRASS method, we analyzed 197 pathways identified from the Kyoto Encyclopedia of Genes and Genomes database. We used the logistic kernel machine (LKM test to identify major contributing genes to each pathway. We conducted functional enrichment analysis of the most significant genes (P<0.01 using the Database for Annotation, Visualization, and Integrated Discovery (DAVID.Two pathways were significantly associated with risk of pancreatic cancer after adjusting for multiple comparisons (P<0.00025 and in replication testing: neuroactive ligand-receptor interaction, (Ps<0.00002, and the olfactory transduction pathway (P = 0.0001. LKM test identified four genes that were significantly associated with risk of pancreatic cancer after Bonferroni correction (P<1×10(-5: ABO, HNF1A, OR13C4, and SHH. Functional enrichment analysis using DAVID consistently found the G protein-coupled receptor signaling pathway (including both neuroactive ligand-receptor interaction and olfactory transduction pathways to be the most significant pathway for pancreatic cancer risk in this study population.These novel findings provide new perspectives on genetic susceptibility to and molecular mechanisms of pancreatic cancer.

  12. Gene profiles between non-invasive and invasive colon cancer using laser microdissection and polypeptide analysis

    Institute of Scientific and Technical Information of China (English)

    Jin-Shui Zhu; Hua Guo; Ming-Quan Song; Guo-Qiang Chen; Qun Sun; Qiang Zhang


    AIM: To explore the expression of differential gene expression profiles of target cell between non-invasive submucosal and invasive advanced tumor in colon carcinoma using laser microdissection (LMD) in combination with polypeptide analysis.METHODS: Normal colon tissue samples from 20 healthy individuals and 30 cancer tissue samples from early non-invasive colon cancer cells were obtained. The cells from these samples were used LMD independently after P27-based amplification. aRNA from advanced colon cancer cells and metastatic cancer cells of 40 cases were applied to LMD and polypeptide analysis, semiquantitative reverse transcribed polymerase chain reaction (RT-PCR) and immunohistochemical assays were used to verify the results of microarray and further identify differentially expressed genes in non-invasive early stages of colon cancer.RESULTS: Five gene expressions were changed in colon carcinoma cells compared with that of controls. Of the five genes, three genes were downregulated and two were upregulated in invasive submucosal colon carcinoma compared with non-invasive cases. The results were confirmed at the level of aRNA and gene expression. Five genes were further identified as differentially expressed genes in the majority of cases (50%, 25/40) in progression of colon cancer, and their expression patterns of which were similar to tumor suppressor genes or oncogenes.CONCLUSION: This study suggested that combined use of polypeptide analysis might identify early expression profiles of five differential genes associated with the invasion of colon cancer. These results reveal that this gene may be a marker of submucosal invasion in early colon cancer.

  13. Scope-Based Method Cache Analysis

    DEFF Research Database (Denmark)

    Huber, Benedikt; Hepp, Stefan; Schoeberl, Martin


    , as it requests memory transfers at well-defined instructions only. In this article, we present a new cache analysis framework that generalizes and improves work on cache persistence analysis. The analysis demonstrates that a global view on the cache behavior permits the precise analyses of caches which are hard......The quest for time-predictable systems has led to the exploration of new hardware architectures that simplify analysis and reasoning in the temporal domain, while still providing competitive performance. For the instruction memory, the method cache is a conceptually attractive solution...

  14. Measuring [{sup 18}F]FDG uptake in breast cancer during chemotherapy: comparison of analytical methods

    Energy Technology Data Exchange (ETDEWEB)

    Krak, Nanda C.; Lammertsma, Adriaan A. [Clinical PET Centre, VU University Medical Centre, De Boelelaan 1117, 1081HV, Amsterdam (Netherlands); Hoeven, Jacobus J.M. van der [Amstelveen Hospital, Amstelveen (Netherlands); Hoekstra, Otto S. [Clinical PET Centre, VU University Medical Centre, De Boelelaan 1117, 1081HV, Amsterdam (Netherlands); Department of Clinical Epidemiology and Biostatistics, VU University Medical Centre, Amsterdam (Netherlands); Twisk, Jos W.R. [Department of Clinical Epidemiology and Biostatistics, VU University Medical Centre, Amsterdam (Netherlands); Wall, Elsken van der [Department of Medical Oncology, VU University Medical Centre, Amsterdam (Netherlands)


    Over the years several analytical methods have been proposed for the measurement of glucose metabolism using fluorine-18 fluorodeoxyglucose ([{sup 18}F]FDG) and positron emission tomography (PET). The purpose of this study was to evaluate which of these (often simplified) methods could potentially be used for clinical response monitoring studies in breast cancer. Prior to chemotherapy, dynamic [{sup 18}F]FDG scans were performed in 20 women with locally advanced (n=10) or metastasised (n=10) breast cancer. Additional PET scans were acquired after 8 days (n=8), and after one, three and six courses of chemotherapy (n=18, 10 and 6, respectively). Non-linear regression (NLR) with the standard two tissue compartment model was used as the gold standard for measurement of [{sup 18}F]FDG uptake and was compared with the following methods: Patlak graphical analysis, simplified kinetic method (SKM), SUV-based net influx constant (''Sadato'' method), standard uptake value [normalised for weight, lean body mass (LBM) and body surface area (BSA), with and without corrections for glucose (g)], tumour to non-tumour ratio (TNT), 6P model and total lesion evaluation (TLE). Correlation coefficients between each analytical method and NLR were calculated using multilevel analysis. In addition, for the most promising methods (Patlak, SKM, SUV{sub LBMg} and SUV{sub BSAg}) it was explored whether correlation with NLR changed with different time points after the start of therapy. Three methods showed excellent correlation (r>0.95) with NLR for the baseline scan: Patlak10-60 and Patlak10-45 (r=0.98 and 0.97, respectively), SKM40-60 (r=0.96) and SUV{sub LBMg} (r=0.96). Good correlation was found between NLR and SUV-based net influx constant, TLE and SUV{sub BSAg} (0.90methods, correlation with NLR

  15. Small-Area Analysis of Incidence and Localisation of Vulvar Cancer

    Directory of Open Access Journals (Sweden)

    Klaus H. Baumann


    Full Text Available Objective. Vulvar cancer is a rare disease mainly in older women. HPV and non-HPV induced vulvar cancer reflect two types of oncogenesis. Controversies exist on most recent developments in vulvar cancer incidence, patients, and disease characteristics. Changes in incidence, age of disease onset, and tumor site in women treated for primary vulvar cancer in a single German university hospital unit will be described. Methods. A retrospective analysis of patient records of women treated between 1994 and 2008 was performed. The fifteen-year-spanning period was divided into three five year-spanning cohorts. Descriptive and statistical analyses were performed. Results. 104 patients were identified: cohort-1 from 1994 to 1998 (11 patients; cohort-2 from 1999 to 2003 (21 patients; cohort-3 from 2004 to 2008 (72 patients. Mean age (years was 73.18 (confidence interval (CI: 64.04; 82.33, 58.9 (CI: 52.24; 65.57, and 61.19 (CI: 57.27; 65.12, respectively. Vulvar cancer confined to the region between clitoris and urethra was seen more often in cohort-3 (=20 compared to cohort-1 (=0 or cohort-2 (=1. Conclusion. This analysis supports the notion of rising incidence of vulvar cancer and a changing pattern of anatomical local extension. Disease onset is not restricted to older women.

  16. Multimodal microscopy for automated histologic analysis of prostate cancer

    Directory of Open Access Journals (Sweden)

    Sinha Saurabh


    Full Text Available Abstract Background Prostate cancer is the single most prevalent cancer in US men whose gold standard of diagnosis is histologic assessment of biopsies. Manual assessment of stained tissue of all biopsies limits speed and accuracy in clinical practice and research of prostate cancer diagnosis. We sought to develop a fully-automated multimodal microscopy method to distinguish cancerous from non-cancerous tissue samples. Methods We recorded chemical data from an unstained tissue microarray (TMA using Fourier transform infrared (FT-IR spectroscopic imaging. Using pattern recognition, we identified epithelial cells without user input. We fused the cell type information with the corresponding stained images commonly used in clinical practice. Extracted morphological features, optimized by two-stage feature selection method using a minimum-redundancy-maximal-relevance (mRMR criterion and sequential floating forward selection (SFFS, were applied to classify tissue samples as cancer or non-cancer. Results We achieved high accuracy (area under ROC curve (AUC >0.97 in cross-validations on each of two data sets that were stained under different conditions. When the classifier was trained on one data set and tested on the other data set, an AUC value of ~0.95 was observed. In the absence of IR data, the performance of the same classification system dropped for both data sets and between data sets. Conclusions We were able to achieve very effective fusion of the information from two different images that provide very different types of data with different characteristics. The method is entirely transparent to a user and does not involve any adjustment or decision-making based on spectral data. By combining the IR and optical data, we achieved high accurate classification.

  17. Cohort Studies on Cancer Mortality Among Workers Exposed Only to Chrysotile Asbestos:a Meta-analysis

    Institute of Scientific and Technical Information of China (English)



    To determine whether there was excessive risk of cancer among workers exposed to chrysotile fiber alone by applying a meta-analysis technique. Methods All data meeting the criteria of cohort studies on cancer mortality among workers exposed only to chrysotile were incorporated into meta-analysis. Pooled standardized mortality ratios (SMRs) and their corresponding 95% confidence intervals (CIs) for main cancer sites were calculated using two approaches of unweighted ratio and random effect model. The heterogeneity and its sources of the results were examined with a Q-statistic and Z-score test. The dose-response effect as reflected in the percentage of all deaths due to mesothelioma served as a proxy measure of chrysotile exposure. Results A cohort of twenty six workers exposed to chrysotile alone was summarized. The significantly elevated meta-SMRs for all deaths (1.27), all cancers (1.28), cancers of respiratory organs (2.51), cancers of lung (2.35) and cancers of stomach (1.24) were observed. The significantly elevated meta-SMRs for lung cancer within occupational strata were observed among textile workers (3.55), asbestos product manufacturers (3.30), miners and millers (2.24), cement product workers (1.22), and for stomach cancer among asbestos product manufacturers (1.49). Meta-SMRs for cancers at other sites were not significant. Meta-SMR for lung cancer showed an increasing trend with an elevated percentage of all deaths from mesothelioma, but no such trend for stomach cancer. Conclusion There are excessive risks of lung cancer and mesothelioma among workers exposed to chrysotile fiber alone, and likely no convincing indication of an etiological association between chrysotile exposure and cancers at other sites.

  18. Biomedical Engineering 2008. New methods for cancer treatment

    Energy Technology Data Exchange (ETDEWEB)

    Vanninen, J.; Koskelainen, A.; Ilmoniemi, R.J. (eds.)


    The report consists of 11 student papers presented in 2008 at the Seminar on Biomedical Engineering at Helsinki University of Technology (Finland). The topics of the seminar included: cancer risk factors and diagnosis, radiation therapy, boron neutron capture treatment (BNCT), chemotherapy, cooling and heating therapy, immunotherapy, angiogenesis inhibition approaches, gene therapy and ablation therapy of liver cancer

  19. 亚甲蓝染色法乳腺癌前哨淋巴结活检术158例分析%Analysis of 158 Cases of Sentinel Lymph Node Biopsy in Breast Cancer by Methylene Blue Staining Method

    Institute of Scientific and Technical Information of China (English)

    黄国兴; 苏国森; 李上芹; 湛建伟; 程少萍


    目的:分析研究亚甲蓝染色法乳腺癌前哨淋巴结活检术(SLNB)158例的检测结果,为临床手术治疗提供数据参考。方法选择乳腺癌患者158例,所有患者均给予亚甲蓝染色法 SLNB 术,观察并统计乳腺癌患者的年龄、肿瘤大小和位置、术前化疗情况以及腋窝淋巴结肿大情况。分析亚甲蓝染色法 SLNB 术对于乳腺癌前哨淋巴结(SLN)的检出情况,并分析影响乳腺癌 SLN 检出的危险因素。结果亚甲蓝染色法 SLNB 术检测乳腺癌SLN 的准确度为94.94%,敏感度为94.38%,特异度为95.65%,肿瘤大小>5 cm 及触及腋窝淋巴结肿大的 SLN 检出率均显著少于肿瘤大小≤5 cm 及未触及腋窝淋巴结肿大者(P 5 cm and hit axillary lymph node enlargement of SLN detection rate were significant-ly less than tumor size≤5 cm and not palpable axillary lymph nodes,the difference was statistically significant (P < 0. 05). Tumor size and axillary lymph nodes were the unfavorable factors for SLN detection in breast cancer. Conclusion Meth-ylene blue staining method was applied to SLNB operation,the detection value was higher,but the clinic should also pay at-tention to the unfavorable factors of SLN detection in breast cancer.

  20. Proteomic analysis of formalin-fixed prostate cancer tissue. (United States)

    Hood, Brian L; Darfler, Marlene M; Guiel, Thomas G; Furusato, Bungo; Lucas, David A; Ringeisen, Bradley R; Sesterhenn, Isabell A; Conrads, Thomas P; Veenstra, Timothy D; Krizman, David B


    Proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tissue would enable retrospective biomarker investigations of this vast archive of pathologically characterized clinical samples that exist worldwide. These FFPE tissues are, however, refractory to proteomic investigations utilizing many state of the art methodologies largely due to the high level of covalently cross-linked proteins arising from formalin fixation. A novel tissue microdissection technique has been developed and combined with a method to extract soluble peptides directly from FFPE tissue for mass spectral analysis of prostate cancer (PCa) and benign prostate hyperplasia (BPH). Hundreds of proteins from PCa and BPH tissue were identified, including several known PCa markers such as prostate-specific antigen, prostatic acid phosphatase, and macrophage inhibitory cytokine-1. Quantitative proteomic profiling utilizing stable isotope labeling confirmed similar expression levels of prostate-specific antigen and prostatic acid phosphatase in BPH and PCa cells, whereas the expression of macrophage inhibitory cytokine-1 was found to be greater in PCa as compared with BPH cells.

  1. Current Challenges in Volatile Organic Compounds Analysis as Potential Biomarkers of Cancer

    Directory of Open Access Journals (Sweden)

    Kamila Schmidt


    Full Text Available An early diagnosis and appropriate treatment are crucial in reducing mortality among people suffering from cancer. There is a lack of characteristic early clinical symptoms in most forms of cancer, which highlights the importance of investigating new methods for its early detection. One of the most promising methods is the analysis of volatile organic compounds (VOCs. VOCs are a diverse group of carbon-based chemicals that are present in exhaled breath and biofluids and may be collected from the headspace of these matrices. Different patterns of VOCs have been correlated with various diseases, cancer among them. Studies have also shown that cancer cells in vitro produce or consume specific VOCs that can serve as potential biomarkers that differentiate them from noncancerous cells. This review identifies the current challenges in the investigation of VOCs as potential cancer biomarkers, by the critical evaluation of available matrices for the in vivo and in vitro approaches in this field and by comparison of the main extraction and detection techniques that have been applied to date in this area of study. It also summarises complementary in vivo, ex vivo, and in vitro studies conducted to date in order to try to identify volatile biomarkers of cancer.

  2. Meta-analysis of case-referent studies of specific environmental or occupational pollutants on lung cancer

    Directory of Open Access Journals (Sweden)

    Mahjub H


    Full Text Available BACKGROUND: Meta-analysis is a statistical tool for combining and integrating the results of independent studies of a given scientific issue. The present investigation was initiated to investigate case-referent studies of lung cancer risk from specific environmental and occupational pollutants, using detailed individual exposure data. MATERIALS AND METHODS: To examine the risk of lung cancer associated with environmental and occupational pollutants, a meta-analysis of published case-control studies was undertaken using a random effects model. For this study, the papers were selected for review from electronic search of PubMed, Medline and Google Scholar during 1990-2006. The principal outcome measure was the odds ratio for the risk of lung cancer. Twelve study reports detailing the relationship between the lung cancer and the type of exposure were identified. RESULTS: The odds ratio of asbestos, cooking fuel, cooking fumes, motor and diesel exhaust related to lung cancer were 1.67, 1.99, 2.52 and 1.42 ( P < 0.001, respectively. The odds ratio of metal fumes related to lung cancer was 1.28 (0.001 P < 0.01. The combined odds ratio for the environmental and occupational exposure related to lung cancer was 1.67 ( P < 0.001. CONCLUSIONS: The meta-analysis of the present study shows the magnitude association between asbestos, cooking fumes, cooking fuels, motor and diesel exhaust, with lung cancer risk. Lung cancer risk may be reduced by controlling exposure levels.

  3. Cruciferous vegetable consumption and gastric cancer risk: a meta-analysis of epidemiological studies. (United States)

    Wu, Qi-Jun; Yang, Yang; Wang, Jing; Han, Li-Hua; Xiang, Yong-Bing


    The relationship between consumption of cruciferous vegetables (CV) and risk of gastric cancer has been investigated by many studies, but remains controversial. We carried out a meta-analysis to summarize available evidence from epidemiological studies on this point. Relevant published reports of CV intake and gastric cancer were identified using MEDLINE (PubMed), EMBASE, and Web of Science databases through to the end of September 2012. We pooled the relative risk from individual studies using a fixed- or random-effects model and carried out heterogeneity and publication bias analyses. Sixteen case-control and six prospective studies were included in our analysis. When all studies were pooled, we yielded a significantly inverse association between CV (relative risk = 0.81; 95% confidence interval, 0.75-0.88) intake and gastric cancer risk, with little heterogeneity (Q = 27.27, P = 0.292, I(2) = 12.0%). Specific analysis for cabbage intake yielded similar result. When separately analyzed, case-control studies of CV intake yielded significant results and the results of prospective studies showed borderline statistical significance. Moreover, significant results were consistent for high-quality studies, for North American, European, and Asian studies, for studies on males, and for studies on non-cardia gastric cancer. Findings from this meta-analysis provide evidence that high intake of CV was inversely associated with the risk of gastric cancer and non-cardia gastric cancer in humans. Further studies on other specific CV, food preparation methods, and stratified results by anatomic cancer site and histological type should be extended in the future.

  4. Analysis of Ethnic Admixture in Prostate Cancer (United States)


    5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-06-1-0181 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Cathryn Bock, Ph.D. 5d. PROJECT NUMBER...Our project uses a novel approach to gene discovery with greater power to detect genetic effects, admixture mapping, to identify prostate cancer...available through HapMap . Because ParAllele was out of business when we were ready to genotype, we used a panel of 1536 ancestry informative SNPs

  5. Quantitative method of measuring cancer cell urokinase and metastatic potential (United States)

    Morrison, Dennis R. (Inventor)


    The metastatic potential of tumors can be evaluated by the quantitative detection of urokinase and DNA. The cell sample selected for examination is analyzed for the presence of high levels of urokinase and abnormal DNA using analytical flow cytometry and digital image analysis. Other factors such as membrane associated urokinase, increased DNA synthesis rates and certain receptors can be used in the method for detection of potentially invasive tumors.

  6. New malignancies following cancer of the urinary bladder: analysis of German cancer registry data. (United States)

    Lehnert, M; Kraywinkel, K; Pesch, B; Holleczek, B; Brüning, T


    This analysis aimed at occurrence and distribution patterns of new malignancies following bladder cancer. Standardised incidence ratios (SIRs) were calculated for two German population-based cancer registries of North Rhine-Westphalia (NRW) and Saarland to access risks for subsequent primaries. An elevated risk for secondary cancer of any site but urothelium was observed in NRW men [SIR 1.35, 95% confidence interval (CI) 1.22-1.49]. The corresponding risk in Saarland was not significantly elevated (SIR 1.06, 95% CI 0.97-1.15). In data of both registries excess risks were observed for cancer of the respiratory tract (SIR 1.54, CI 1.23-1.89 in NRW men) and the prostate (SIR 1.91, 95% CI 1.61-2.24 in NRW; SIR 1.25, 95% CI 1.07-1.45 in Saarland). Common risk factors and incidental findings during follow-up care of bladder cancer patients might explain most of the observed patterns. In addition SIRs were throughout particular high for subsequent cancer of the renal pelvis and the ureter due to pathological characteristics of urothelial neoplasms.

  7. Transcriptional master regulator analysis in breast cancer genetic networks. (United States)

    Tovar, Hugo; García-Herrera, Rodrigo; Espinal-Enríquez, Jesús; Hernández-Lemus, Enrique


    Gene regulatory networks account for the delicate mechanisms that control gene expression. Under certain circumstances, gene regulatory programs may give rise to amplification cascades. Such transcriptional cascades are events in which activation of key-responsive transcription factors called master regulators trigger a series of gene expression events. The action of transcriptional master regulators is then important for the establishment of certain programs like cell development and differentiation. However, such cascades have also been related with the onset and maintenance of cancer phenotypes. Here we present a systematic implementation of a series of algorithms aimed at the inference of a gene regulatory network and analysis of transcriptional master regulators in the context of primary breast cancer cells. Such studies were performed in a highly curated database of 880 microarray gene expression experiments on biopsy-captured tissue corresponding to primary breast cancer and healthy controls. Biological function and biochemical pathway enrichment analyses were also performed to study the role that the processes controlled - at the transcriptional level - by such master regulators may have in relation to primary breast cancer. We found that transcription factors such as AGTR2, ZNF132, TFDP3 and others are master regulators in this gene regulatory network. Sets of genes controlled by these regulators are involved in processes that are well-known hallmarks of cancer. This kind of analyses may help to understand the most upstream events in the development of phenotypes, in particular, those regarding cancer biology.

  8. Advanced analysis methods in particle physics

    Energy Technology Data Exchange (ETDEWEB)

    Bhat, Pushpalatha C.; /Fermilab


    Each generation of high energy physics experiments is grander in scale than the previous - more powerful, more complex and more demanding in terms of data handling and analysis. The spectacular performance of the Tevatron and the beginning of operations of the Large Hadron Collider, have placed us at the threshold of a new era in particle physics. The discovery of the Higgs boson or another agent of electroweak symmetry breaking and evidence of new physics may be just around the corner. The greatest challenge in these pursuits is to extract the extremely rare signals, if any, from huge backgrounds arising from known physics processes. The use of advanced analysis techniques is crucial in achieving this goal. In this review, I discuss the concepts of optimal analysis, some important advanced analysis methods and a few examples. The judicious use of these advanced methods should enable new discoveries and produce results with better precision, robustness and clarity.

  9. Advanced Analysis Methods in Particle Physics

    Energy Technology Data Exchange (ETDEWEB)

    Bhat, Pushpalatha C. [Fermilab


    Each generation of high energy physics experiments is grander in scale than the previous – more powerful, more complex and more demanding in terms of data handling and analysis. The spectacular performance of the Tevatron and the beginning of operations of the Large Hadron Collider, have placed us at the threshold of a new era in particle physics. The discovery of the Higgs boson or another agent of electroweak symmetry breaking and evidence of new physics may be just around the corner. The greatest challenge in these pursuits is to extract the extremely rare signals, if any, from huge backgrounds arising from known physics processes. The use of advanced analysis techniques is crucial in achieving this goal. In this review, I discuss the concepts of optimal analysis, some important advanced analysis methods and a few examples. The judicious use of these advanced methods should enable new discoveries and produce results with better precision, robustness and clarity.

  10. Application of Software Safety Analysis Methods

    Energy Technology Data Exchange (ETDEWEB)

    Park, G. Y.; Hur, S.; Cheon, S. W.; Kim, D. H.; Lee, D. Y.; Kwon, K. C. [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Lee, S. J.; Koo, Y. H. [Doosan Heavy Industries and Construction Co., Daejeon (Korea, Republic of)


    A fully digitalized reactor protection system, which is called the IDiPS-RPS, was developed through the KNICS project. The IDiPS-RPS has four redundant and separated channels. Each channel is mainly composed of a group of bistable processors which redundantly compare process variables with their corresponding setpoints and a group of coincidence processors that generate a final trip signal when a trip condition is satisfied. Each channel also contains a test processor called the ATIP and a display and command processor called the COM. All the functions were implemented in software. During the development of the safety software, various software safety analysis methods were applied, in parallel to the verification and validation (V and V) activities, along the software development life cycle. The software safety analysis methods employed were the software hazard and operability (Software HAZOP) study, the software fault tree analysis (Software FTA), and the software failure modes and effects analysis (Software FMEA)

  11. Evaluation of prostate cancer antigen 3 for detecting prostate cancer: a systematic review and meta-analysis (United States)

    Cui, Yong; Cao, Wenzhou; Li, Quan; Shen, Hua; Liu, Chao; Deng, Junpeng; Xu, Jiangfeng; Shao, Qiang


    Previous studies indicate that prostate cancer antigen 3 (PCA3) is highly expressed in prostatic tumors. However, its clinical value has not been characterized. The aim of this study was to investigate the clinical value of the urine PCA3 test in the diagnosis of prostate cancer by pooling the published data. Clinical trials utilizing the urine PCA3 test for diagnosing prostate cancer were retrieved from PubMed and Embase. A total of 46 clinical trials including 12,295 subjects were included in this meta-analysis. The pooled sensitivity, specificity, positive likelihood ratio (+LR), negative likelihood ratio (‑LR), diagnostic odds ratio (DOR) and area under the curve (AUC) were 0.65 (95% confidence interval [CI]: 0.63–0.66), 0.73 (95% CI: 0.72–0.74), 2.23 (95% CI: 1.91–2.62), 0.48 (95% CI: 0.44–0.52), 5.31 (95% CI: 4.19–6.73) and 0.75 (95% CI: 0.74–0.77), respectively. In conclusion, the urine PCA3 test has acceptable sensitivity and specificity for the diagnosis of prostate cancer and can be used as a non-invasive method for that purpose.

  12. Analysis of mixed data methods & applications

    CERN Document Server

    de Leon, Alexander R


    A comprehensive source on mixed data analysis, Analysis of Mixed Data: Methods & Applications summarizes the fundamental developments in the field. Case studies are used extensively throughout the book to illustrate interesting applications from economics, medicine and health, marketing, and genetics. Carefully edited for smooth readability and seamless transitions between chaptersAll chapters follow a common structure, with an introduction and a concluding summary, and include illustrative examples from real-life case studies in developmental toxicolog

  13. Proteome of human colon cancer stem cells: A comparative analysis

    Institute of Scientific and Technical Information of China (English)

    Jian Zou; Xiao-Feng Yu; Zhi-Jun Bao; Jie Dong


    AIM: To isolate and identify the biological characteristics of human colon cancer stem cells (SW1116 cells) and further study their proteome. METHODS: SW1116 cells were isolated and cultured with a serum-free medium (SFM). Sphere formation was assayed to observe the formation of colon cancer stem cell spheres. SW1116 cells were inoculated into a serum-containing medium for observing their differentiation characteristics. Proliferation curve and cross-resistance of SW1116 cells to different drugs were detected by MTT. Percentage of SP cells in SW1116 cells was detected with Hoechst33342 staining. Telomerase activity in SW1116cells was checked by polymerase chain reaction (PCR)-enzyme linked immunosorbent assay. Expressions of stem cell relevant genes and proteins were detected by reverse transcription-PCR and Western blot, respectively. Total protein was isolated from SW1116 cells by two-dimensional gel electrophoresis (2-DE) and differentially expressed proteins were identified by tandem mass spectrometry (MALDI-TOF/TOF). RESULTS: The isolated SW1116 cells presented as spheroid and suspension growths in SFM with a strong self-renewal, proliferation, differentiation and drug-resistance ability. The percentage of SP cells in SW1116 cells was 38.9%. The SW1116 cells co-expressed the CD133 and CD29 proteins. The telomerase activity in SW1116 cells was increased. The expressions of different stem cell relevant genes and proteins were detected. The proteomic analysis showed that the 26 protein spots were differently expressed in SW1116 cells and 10 protein spots were identified as ubiquitin fusiondegradation 1-like protein, nuclear chloride channel protein, tubulin b, Raichu404X, stratifin, F-actin capping protein a-1 subunit, eukaryotic translation elongation factor 1 delta isoform 2, hypothetical protein, glyceraldehyde-3-phosphate dehydrogenase and guanine nucleotide binding protein b polypeptide 2-like 1, respectively. CONCLUSION: SW1116 cells are biologically

  14. Machine learning methods in the computational biology of cancer. (United States)

    Vidyasagar, M


    The objectives of this Perspective paper are to review some recent advances in sparse feature selection for regression and classification, as well as compressed sensing, and to discuss how these might be used to develop tools to advance personalized cancer therapy. As an illustration of the possibilities, a new algorithm for sparse regression is presented and is applied to predict the time to tumour recurrence in ovarian cancer. A new algorithm for sparse feature selection in classification problems is presented, and its validation in endometrial cancer is briefly discussed. Some open problems are also presented.

  15. TLR3 gene polymorphisms in cancer:a systematic review and meta-analysis

    Institute of Scientific and Technical Information of China (English)

    Ben-Gang Wang; De-Hui Yi; Yong-Feng Liu


    Introduction:Recent studies examining the association of Toll-like receptor 3 ( TLR3) gene polymorphisms with the risk of developing various types of cancer have reported conflicting results. Clarifying this association could advance our knowledge of the influence of TLR3 single nucleotide polymorphisms (SNPs) on cancer risk. Methods:We systematically reviewed studies that focused on a collection of 12 SNPs located in the TLR3 gene and the details by which these SNPs influenced cancer risk. Additionally, 14 case-control studies comprising a total of 7997 cases of cancer and 8699 controls were included in a meta-analysis of 4 highly studied SNPs (rs3775290, rs3775291, rs3775292, and rs5743312). Results:The variant TLR3 genotype rs5743312 (C9948T, intron 3, C>T) was significantly associated with an increased cancer risk as compared with the wild-type allele (odds ratio [OR]=1.11, 95%confidence interval [CI]=1.00–1.24, P=0.047). No such association was observed with other TLR3 SNPs. In the stratified analysis, the rs3775290 (C13766T, C>T) variant genotype was found to be significantly associated with an increased cancer risk in Asian populations. Additional y, the rs3775291 (G13909A, G>A) variant genotype was significantly associated with an increased cancer risk in Asians, subgroup with hospital-based controls, and subgroup with a smal sample size. Conclusion:After data integration, our findings suggest that the TLR3 rs5743312 polymorphism may contribute to an increased cancer risk.

  16. Chromatographic methods for analysis of triazine herbicides. (United States)

    Abbas, Hana Hassan; Elbashir, Abdalla A; Aboul-Enein, Hassan Y


    Gas chromatography (GC) and high-performance liquid chromatography (HPLC) coupled to different detectors, and in combination with different sample extraction methods, are most widely used for analysis of triazine herbicides in different environmental samples. Nowadays, many variations and modifications of extraction and sample preparation methods such as solid-phase microextraction (SPME), hollow fiber-liquid phase microextraction (HF-LPME), stir bar sportive extraction (SBSE), headspace-solid phase microextraction (HS-SPME), dispersive liquid-liquid microextraction (DLLME), dispersive liquid-liquid microextraction based on solidification of floating organic droplet (DLLME-SFO), ultrasound-assisted emulsification microextraction (USAEME), and others have been introduced and developed to obtain sensitive and accurate methods for the analysis of these hazardous compounds. In this review, several analytical properties such as linearity, sensitivity, repeatability, and accuracy for each developed method are discussed, and excellent results were obtained for the most of developed methods combined with GC and HPLC techniques for the analysis of triazine herbicides. This review gives an overview of recent publications of the application of GC and HPLC for analysis of triazine herbicides residues in various samples.

  17. Pancreatic Cancer in a Northern African Population: A Retrospective Analysis Spanning Two Decades

    Directory of Open Access Journals (Sweden)

    Feriel Sellam


    Full Text Available Background Pancreatic cancer has the highest mortality rate of all major cancers. 94% of pancreatic cancer patients will die within five years of diagnosis. Objective To study the epidemiological and pathological characteristics of pancreatic cancer in North African population over a period of twenty two years from 1991 to 2013. Patients and method This was an epidemiological descriptive study conducted in Sidi bel Abbes University Hospital (Western Algeria, Northern Africa. We made a retrospective analysis of records of patients diagnosed with pancreatic cancer and for this purpose the study period was sub-classified into two periods: 1991-2002 and 2003-2013. Results 264 patients aged between 16-96 years were diagnosed with pancreatic cancer; 107 females (40.5% and 157 males (59.5% were recorded between 1991 and 2013; with a sex ratio of 1.46, and age range 16–96 years (median 66.2. Ninety patients (34% were diagnosed with pancreatic cancer during the first period (1991-2002, and 147 patients (66% during the second one (2003 – 2013. A significant association was reported between male patients and their medical histories in the second period (p=0.012; 29% of those patients suffered from diabetes mellitus and 23% from high blood pressure. Another significant correlation was noted between male gender and TNM classification during the first period where p=0.047, mainly at M1 and T4 stages with respectively the rates of 26.3% and 19.3%. Conclusion Pancreatic cancer remains one of the deadliest cancers worldwide and even in developing countries.

  18. Association between alcohol consumption and cancers in the Chinese population--a systematic review and meta-analysis.

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    Ying Li

    Full Text Available BACKGROUND: Alcohol consumption is increasing worldwide and is associated with numerous cancers. This systematic review examined the role of alcohol in the incidence of cancer in the Chinese population. METHODS: Medline/PubMed, EMBASE, CNKI and VIP were searched to identify relevant studies. Cohort and case-control studies on the effect of alcohol use on cancers in Chinese were included. Study quality was evaluated using the Newcastle-Ottawa Scale. Data were independently abstracted by two reviewers. Odds ratios (OR or relative risks (RR were pooled using RevMan 5.0. Heterogeneity was evaluated using the Q test and I-squared statistic. P<.01 was considered statistically significant. RESULTS: Pooled results from cohort studies indicated that alcohol consumption was not associated with gastric cancer, esophageal cancers (EC or lung cancer. Meta-analysis of case-control studies showed that alcohol consumption was a significant risk factor for five cancers; the pooled ORs were 1.79 (99% CI, 1.47-2.17 EC, 1.40 (99% CI, 1.19-1.64 gastric cancer, 1.56 (99% CI, 1.16-2.09 hepatocellular carcinoma, 1.21 (99% CI, 1.00-1.46 nasopharyngeal cancer and 1.71 (99% CI, 1.20-2.44 oral cancer. Pooled ORs of the case-control studies showed that alcohol consumption was protective for female breast cancer and gallbladder cancer: OR 0.76 (99% CI, 0.60-0.97 and 0.70 (99% CI, 0.49-1.00 respectively. There was no significant correlation between alcohol consumption and lung cancer, colorectal cancer, pancreatic cancer, cancer of the ampulla of Vater, prostate cancer or extrahepatic cholangiocarcinoma. Combined results of case-control and cohort studies showed that alcohol consumption was associated with 1.78- and 1.40-fold higher risks of EC and gastric cancer but was not significantly associated with lung cancer. CONCLUSIONS: Health programs focused on limiting alcohol intake may be important for cancer control in China. Further studies are needed to examine the

  19. Novel Molecular and Computational Methods Improve the Accuracy of Insertion Site Analysis in Sleeping Beauty-Induced Tumors


    Benjamin T Brett; Katherine E Berquam-Vrieze; Kishore Nannapaneni; Jian Huang; Todd E Scheetz; Dupuy, Adam J.


    The recent development of the Sleeping Beauty (SB) system has led to the development of novel mouse models of cancer. Unlike spontaneous models, SB causes cancer through the action of mutagenic transposons that are mobilized in the genomes of somatic cells to induce mutations in cancer genes. While previous methods have successfully identified many transposon-tagged mutations in SB-induced tumors, limitations in DNA sequencing technology have prevented a comprehensive analysis of large tumor ...

  20. An introduction to numerical methods and analysis

    CERN Document Server

    Epperson, J F


    Praise for the First Edition "". . . outstandingly appealing with regard to its style, contents, considerations of requirements of practice, choice of examples, and exercises.""-Zentrablatt Math "". . . carefully structured with many detailed worked examples . . .""-The Mathematical Gazette "". . . an up-to-date and user-friendly account . . .""-Mathematika An Introduction to Numerical Methods and Analysis addresses the mathematics underlying approximation and scientific computing and successfully explains where approximation methods come from, why they sometimes work (or d

  1. Lung Cancer Susceptibility and hOGG1 Ser326Cys Polymorphism: A Meta-Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kiyohara, Chikako, E-mail: [Department of Preventive Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan); Takayama, Koichi; Nakanishi, Yoichi [Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan)


    Recent lung cancer studies have focused on identifying the effects of single nucleotide polymorphisms (SNPs) in candidate genes, among which DNA repair genes are increasingly being studied. Genetic variations in DNA repair genes are thought to modulate DNA repair capacity and are suggested to be related to lung cancer risk. In this study, we tried to assess reported studies of association between polymorphism of human 8-oxoguanine DNA glycosylase 1 (hOGG1) Ser326Cys and lung cancer. We conducted MEDLINE, Current Contents and Web of Science searches using 'hOGG1', 'lung cancer' and 'polymorphism' as keywords to search for papers published (from January 1995 through August 2010). Data were combined using both a fixed effects (the inverse variance-weighted method) and a random effects (DerSimonian and Laird method) models. The Cochran Q test was used for the assessment of heterogeneity. Publication bias was assessed by both Begg’s and Egger’s tests. We identified 20 case-control studies in 21 different ethnic populations. As two studies were not in the Hardy-Weinberg equilibrium, 18 case-control studies in 19 different ethnic populations (7,792 cases and 9,358 controls) were included in our meta-analysis. Summary frequencies of the Cys allele among Caucasians and Asians based on the random effects model were 20.9% (95% confidence interval (CI) = 18.9–22.9) and 46.1% (95% CI = 40.2–52.0), respectively. The distribution of the Cys allele was significantly different between Asians and Caucasians (P < 0.001). The Cys/Cys genotype was significantly associated with lung cancer risk in Asian populations (odds ratio = 1.27, 95% CI = 1.09–1.48) but not in Caucasian populations. This ethnic difference in lung cancer risk may be due to environmental factors such as cigarette smoking and dietary factors. Although the summary risk for developing lung cancer may not be large, lung cancer is such a common malignancy that even a small increase

  2. Analysis on Lung Cancer Survival from 2001 to 2007 in Qidong, China

    Directory of Open Access Journals (Sweden)

    Jian ZHU


    Full Text Available Background and objective Lung cancer is one of the most important malignancies in China. Survival rates of lung cancer on the population-based cancer registry for the years 2001-2007 in Qidong were analysed in order to provide the basis for the prognosis assessment and the control of this cancer. Methods Total 4,451 registered lung cancer cases was followed up to December 31st, 2009. Death certificates only (DCO cases were excluded, leaving 4,382 cases for survival analysis. Cumulative observed survival rate (OS and relative survival rate (RS were calculated using Hakulinen’s method performed by the SURV 3.01 software developed at the Finnish Cancer Registry. Results The 1-, 3-, and 5-year OS rates were 23.73%, 11.89%, 10.01%, and the RS rates were 24.86%, 13.69%, 12.73%, respectively. The 1-, 3-, and 5-year RS of males vs females were 23.70% vs 27.89%, 12.58% vs 16.53%, and 11.73% vs 15.21%, respectively, with statisitically significant differences (χ2=13.77, P=0.032. RS of age groups of 15-34, 35-44, 45-54, 55-64, 65-74 and 75+ were 35.46%, 17.66%, 11.97%, 13.49%, 10.61%, 15.14%, respectively. Remarkable improvement could be seen for the 5-year RS in this setting if compared with that for the years 1972-2000. Conclusion The lung cancer survival outcomes in Qidong have been improved gradually for the past decades. Further measures on the prevention, diagnosis and treatment of lung cancer should be taken.

  3. Methods for genetic linkage analysis using trisomies

    Energy Technology Data Exchange (ETDEWEB)

    Feingold, E. [Emory Univ. School of Public Health, Atlanta, GA (United States); Lamb, N.E.; Sherman, S.L. [Emory Univ., Atlanta, GA (United States)


    Certain genetic disorders are rare in the general population, but more common in individuals with specific trisomies. Examples of this include leukemia and duodenal atresia in trisomy 21. This paper presents a linkage analysis method for using trisomic individuals to map genes for such traits. It is based on a very general gene-specific dosage model that posits that the trait is caused by specific effects of different alleles at one or a few loci and that duplicate copies of {open_quotes}susceptibility{close_quotes} alleles inherited from the nondisjoining parent give increased likelihood of having the trait. Our mapping method is similar to identity-by-descent-based mapping methods using affected relative pairs and also to methods for mapping recessive traits using inbred individuals by looking for markers with greater than expected homozygosity by descent. In the trisomy case, one would take trisomic individuals and look for markers with greater than expected homozygosity in the chromosomes inherited from the nondisjoining parent. We present statistical methods for performing such a linkage analysis, including a test for linkage to a marker, a method for estimating the distance from the marker to the trait gene, a confidence interval for that distance, and methods for computing power and sample sizes. We also resolve some practical issues involved in implementing the methods, including how to use partially informative markers and how to test candidate genes. 20 refs., 5 figs., 1 tab.

  4. Dietary Patterns and Pancreatic Cancer Risk: A Meta-Analysis (United States)

    Lu, Pei-Ying; Shu, Long; Shen, Shan-Shan; Chen, Xu-Jiao; Zhang, Xiao-Yan


    A number of studies have examined the associations between dietary patterns and pancreatic cancer risk, but the findings have been inconclusive. Herein, we conducted this meta-analysis to assess the associations between dietary patterns and the risk of pancreatic cancer. MEDLINE (provided by the National Library of Medicine) and EBSCO (Elton B. Stephens Company) databases were searched for relevant articles published up to May 2016 that identified common dietary patterns. Thirty-two studies met the inclusion criteria and were finally included in this meta-analysis. A reduced risk of pancreatic cancer was shown for the highest compared with the lowest categories of healthy patterns (odds ratio, OR = 0.86; 95% confidence interval, CI: 0.77–0.95; p = 0.004) and light–moderate drinking patterns (OR = 0.90; 95% CI: 0.83–0.98; p = 0.02). There was evidence of an increased risk for pancreatic cancer in the highest compared with the lowest categories of western-type pattern (OR = 1.24; 95% CI: 1.06–1.45; p = 0.008) and heavy drinking pattern (OR = 1.29; 95% CI: 1.10–1.48; p = 0.002). The results of this meta-analysis demonstrate that healthy and light–moderate drinking patterns may decrease the risk of pancreatic cancer, whereas western-type and heavy drinking patterns may increase the risk of pancreatic cancer. Additional prospective studies are needed to confirm these findings. PMID:28067765

  5. Detection of somatic mutations by high-resolution DNA melting (HRM analysis in multiple cancers.

    Directory of Open Access Journals (Sweden)

    Jesus Gonzalez-Bosquet

    Full Text Available Identification of somatic mutations in cancer is a major goal for understanding and monitoring the events related to cancer initiation and progression. High resolution melting (HRM curve analysis represents a fast, post-PCR high-throughput method for scanning somatic sequence alterations in target genes. The aim of this study was to assess the sensitivity and specificity of HRM analysis for tumor mutation screening in a range of tumor samples, which included 216 frozen pediatric small rounded blue-cell tumors as well as 180 paraffin-embedded tumors from breast, endometrial and ovarian cancers (60 of each. HRM analysis was performed in exons of the following candidate genes known to harbor established commonly observed mutations: PIK3CA, ERBB2, KRAS, TP53, EGFR, BRAF, GATA3, and FGFR3. Bi-directional sequencing analysis was used to determine the accuracy of the HRM analysis. For the 39 mutations observed in frozen samples, the sensitivity and specificity of HRM analysis were 97% and 87%, respectively. There were 67 mutation/variants in the paraffin-embedded samples, and the sensitivity and specificity for the HRM analysis were 88% and 80%, respectively. Paraffin-embedded samples require higher quantity of purified DNA for high performance. In summary, HRM analysis is a promising moderate-throughput screening test for mutations among known candidate genomic regions. Although the overall accuracy appears to be better in frozen specimens, somatic alterations were detected in DNA extracted from paraffin-embedded samples.

  6. Development of a Standardized Method for Contouring the Lumbosacral Plexus: A Preliminary Dosimetric Analysis of this Organ at Risk Among 15 Patients Treated With Intensity-Modulated Radiotherapy for Lower Gastrointestinal Cancers and the Incidence of Radiation-Induced Lumbosacral Plexopathy

    Energy Technology Data Exchange (ETDEWEB)

    Yi, Sun K., E-mail: [Department of Radiation Oncology, University of California, Davis Cancer Center, Sacramento, CA (United States); Mak, Walter [Department of Radiology, University of California, Davis Medical Center, Sacramento, CA (United States); Yang, Claus C.; Liu Tianxiao [Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS (United States); Cui Jing; Chen, Allen M.; Purdy, James A.; Monjazeb, Arta M. [Department of Radiation Oncology, University of California, Davis Cancer Center, Sacramento, CA (United States); Do, Ly [Cancer Care Institute, San Jose, CA (United States)


    Purpose: To generate a reproducible step-wise guideline for the delineation of the lumbosacral plexus (LSP) on axial computed tomography (CT) planning images and to provide a preliminary dosimetric analysis on 15 representative patients with rectal or anal cancers treated with an intensity-modulated radiotherapy (IMRT) technique. Methods and Materials: A standardized method for contouring the LSP on axial CT images was devised. The LSP was referenced to identifiable anatomic structures from the L4-5 interspace to the level of the sciatic nerve. It was then contoured retrospectively on 15 patients treated with IMRT for rectal or anal cancer. No dose limitations were placed on this organ at risk during initial treatment planning. Dosimetric parameters were evaluated. The incidence of radiation-induced lumbosacral plexopathy (RILSP) was calculated. Results: Total prescribed dose to 95% of the planned target volume ranged from 50.4 to 59.4 Gy (median 54 Gy). The mean ({+-}standard deviation [SD]) LSP volume for the 15 patients was 100 {+-} 22 cm{sup 3} (range, 71-138 cm{sup 3}). The mean maximal dose to the LSP was 52.6 {+-} 3.9 Gy (range, 44.5-58.6 Gy). The mean irradiated volumes of the LSP were V40Gy = 58% {+-} 19%, V50Gy = 22% {+-} 23%, and V55Gy = 0.5% {+-} 0.9%. One patient (7%) was found to have developed RILSP at 13 months after treatment. Conclusions: The true incidence of RILSP in the literature is likely underreported and is not a toxicity commonly assessed by radiation oncologists. In our analysis the LSP commonly received doses approaching the prescribed target dose, and 1 patient developed RILSP. Identification of the LSP during IMRT planning may reduce RILSP. We have provided a reproducible method for delineation of the LSP on CT images and a preliminary dosimetric analysis for potential future dose constraints.

  7. Shortened telomere length is associated with increased risk of cancer: a meta-analysis.

    Directory of Open Access Journals (Sweden)

    Hongxia Ma

    Full Text Available BACKGROUND: Telomeres play a key role in the maintenance of chromosome integrity and stability, and telomere shortening is involved in initiation and progression of malignancies. A series of epidemiological studies have examined the association between shortened telomeres and risk of cancers, but the findings remain conflicting. METHODS: A dataset composed of 11,255 cases and 13,101 controls from 21 publications was included in a meta-analysis to evaluate the association between overall cancer risk or cancer-specific risk and the relative telomere length. Heterogeneity among studies and their publication bias were further assessed by the χ(2-based Q statistic test and Egger's test, respectively. RESULTS: The results showed that shorter telomeres were significantly associated with cancer risk (OR = 1.35, 95% CI = 1.14-1.60, compared with longer telomeres. In the stratified analysis by tumor type, the association remained significant in subgroups of bladder cancer (OR = 1.84, 95% CI = 1.38-2.44, lung cancer (OR = 2.39, 95% CI = 1.18-4.88, smoking-related cancers (OR = 2.25, 95% CI = 1.83-2.78, cancers in the digestive system (OR = 1.69, 95% CI = 1.53-1.87 and the urogenital system (OR = 1.73, 95% CI = 1.12-2.67. Furthermore, the results also indicated that the association between the relative telomere length and overall cancer risk was statistically significant in studies of Caucasian subjects, Asian subjects, retrospective designs, hospital-based controls and smaller sample sizes. Funnel plot and Egger's test suggested that there was no publication bias in the current meta-analysis (P = 0.532. CONCLUSIONS: The results of this meta-analysis suggest that the presence of shortened telomeres may be a marker for susceptibility to human cancer, but single larger, well-design prospective studies are warranted to confirm these findings.

  8. Association between Helicobacter pylori Infection and Pancreatic Cancer. A Cumulative Meta-Analysis

    Directory of Open Access Journals (Sweden)

    Guru Trikudanathan


    Full Text Available Context Infection with Helicobacter pylori (H. pylori has been implicated in the etiopathogenesis of various malignant conditions. Notwithstanding, its etiological association with pancreatic cancer remains inconclusive. Studies focusing on the relationship between H. pylori infection and pancreatic cancer risk have yielded conflicting results. Objective The aim of this study was to obtain a reliable estimate of the risk of H. pylori infection in causing pancreatic cancer, by performing a meta-analysis of the existing observational studies evaluating the association. Methods/Statistics Observational studies comparing the prevalence of H. pylori infection in patients with pancreatic cancer and healthy controls, conducted in adult populations and published in all languages, were identified through systematic search in the MEDLINE and EMBASE up to April 2010. H. pylori infection was confirmed by serological testing using an antigen-specific enzyme-linked immunosorbent assay. Pooled adjusted odds ratios (AOR and associated 95% confidence intervals (CI were obtained by using a DerSimonian and Laird random-effects model. Results Six studies involving a total of 2,335 patients met our eligibility criteria. A significant association between H. pylori seropositivity and development of pancreatic cancer (AOR 1.38, 95% CI: 1.08-1.75; P=0.009 was seen. No significant association was seen on pooled analysis of the three studies assessing the relationship between cytotoxin-associated gene A (CagA positivity and pancreatic cancer. A cumulative meta-analysis suggested a reducing, albeit statistically significant association as the evidence was accumulated. Conclusions The pooled data suggests an association between infection with H. pylori and the development of pancreatic cancer. Further research is needed to confirm our findings.

  9. Association between CD14 gene polymorphisms and cancer risk: a meta-analysis.

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    Jun Wang

    Full Text Available BACKGROUND: Two polymorphisms, -260C/T and -651C/T, in the CD14 gene have been implicated in susceptibility to cancer. However, the results remain inconclusive. This meta-analysis aimed to investigate the association between the two polymorphisms and risk of cancer. METHODS: All eligible case-control studies published up to March 2014 were identified by searching PubMed, Web of Science, CNKI and WanFang database. Pooled odds ratio (OR with 95% confidence interval (CI were used to access the strength of this association in fixed- or random-effects model. RESULTS: 17 case-control studies from fourteen articles were included. Of those, there were 17 studies (4198 cases and 4194 controls for -260C/T polymorphism and three studies (832 cases and 1190 controls for -651C/T polymorphism. Overall, no significant associations between the two polymorphisms of CD14 gene and cancer risk were found. When stratified by ethnicity, cancer type and source of control, similar results were observed among them. In addition, in further subgroups analysis by Helicobacter pylori (H. pylori infection status and tumor location in gastric cancer subgroup, we found that the CD14 -260C/T polymorphism may increase the risk of gastric cancer in H. pylori-infected individuals. CONCLUSIONS: This meta-analysis suggests that the CD14 -260C/T polymorphism may increase the risk of gastric cancer in H. pylori-infected individuals. However, large and well-designed studies are warranted to validate our findings.

  10. Genes-environment interactions in obesity- and diabetes-associated pancreatic cancer: A GWAS data analysis (United States)

    Tang, Hongwei; Wei, Peng; Duell, Eric J.; Risch, Harvey A.; Olson, Sara H.; Bueno-de-Mesquita, H. Bas; Gallinger, Steven; Holly, Elizabeth A.; Petersen, Gloria M.; Bracci, Paige M.; McWilliams, Robert R.; Jenab, Mazda; Riboli, Elio; Tjønneland, Anne; Boutron-Ruault, Marie Christine; Kaaks, Rudolf; Trichopoulos, Dimitrios; Panico, Salvatore; Sund, Malin; Peeters, Petra H.M; Khaw, Kay-Tee; Amos, Christopher I; Li, Donghui


    Background Obesity and diabetes are potentially alterable risk factors for pancreatic cancer. Genetic factors that modify the associations of obesity and diabetes with pancreatic cancer have previously not been examined at the genome-wide level. Methods Using GWAS genotype and risk factor data from the Pancreatic Cancer Case Control Consortium, we conducted a discovery study of 2,028 cases and 2,109 controls to examine gene-obesity and gene-diabetes interactions in relation to pancreatic cancer risk by employing the likelihood ratio test (LRT) nested in logistic regression models and Ingenuity Pathway Analysis (IPA). Results After adjusting for multiple comparisons, a significant interaction of the chemokine signaling pathway with obesity (P = 3.29 × 10−6) and a near significant interaction of calcium signaling pathway with diabetes (P = 1.57 × 10−4) in modifying the risk of pancreatic cancer was observed. These findings were supported by results from IPA analysis of the top genes with nominal interactions. The major contributing genes to the two top pathways include GNGT2, RELA, TIAM1 and GNAS. None of the individual genes or SNPs except one SNP remained significant after adjusting for multiple testing. Notably, SNP rs10818684 of the PTGS1 gene showed an interaction with diabetes (P = 7.91 × 10−7) at a false discovery rate of 6%. Conclusions Genetic variations in inflammatory response and insulin resistance may affect the risk of obesity and diabetes-related pancreatic cancer. These observations should be replicated in additional large datasets. Impact Gene-environment interaction analysis may provide new insights into the genetic susceptibility and molecular mechanisms of obesity- and diabetes-related pancreatic cancer. PMID:24136929

  11. Objective Diagnosis of Cervical Cancer by Tissue Protein Profile Analysis (United States)

    Patil, Ajeetkumar; Bhat, Sujatha; Rai, Lavanya; Kartha, V. B.; Chidangil, Santhosh


    Protein profiles of homogenized normal cervical tissue samples from hysterectomy subjects and cancerous cervical tissues from biopsy samples collected from patients with different stages of cervical cancer were recorded using High Performance Liquid Chromatography coupled with Laser Induced Fluorescence (HPLC-LIF). The Protein profiles were subjected to Principle Component Analysis to derive statistically significant parameters. Diagnosis of sample types were carried out by matching three parameters—scores of factors, squared residuals, and Mahalanobis Distance. ROC and Youden's Index curves for calibration standards were used for objective estimation of the optimum threshold for decision making and performance.

  12. Epidemiology of Cancers in Kashmir, India: An Analysis of Hospital Data. (United States)

    Qurieshi, Mariya A; Khan, S M Salim; Masoodi, Muneer A; Qurieshi, Uruj; Ain, Quratul; Jan, Yasmeen; Haq, Inaamul; Ahmad, Sheikh Zahoor


    Cancer is a leading cause of mortality and morbidity in the world. The aim of the present study was to measure the pattern of different cancers in Kashmir, India, a cancer belt with peculiar cancer profile. A hospital based cancer registry was started by the Department of Community Medicine, Government Medical College, Srinagar, in January 2006, wherein information was collected from cancer patients who were diagnosed and treated in the hospital. Data has been analysed for a period extending from January 2006 to December 2012. Descriptive analysis has been done by using statistical software. A total of 1598 cancer patients were admitted during this period. Overall male to female ratio was 1.33 : 1. Stomach cancer was the most commonly reported cancer (25.2%), followed by colorectal cancer (16.4%) and lung cancer (13.2%) among males. For females, colorectal cancer (16.8%), breast cancer (16.1%), and stomach cancer (10.4%) were the most frequently reported cancers in order of frequency. Tobacco related cancers contributed to more than three-fourths of cancers among men and more than half of cancers for women. There is an urgent need to set up a population based cancer registration system to understand the profile of cancers specific to this geographic region.

  13. Epidemiology of Cancers in Kashmir, India: An Analysis of Hospital Data

    Directory of Open Access Journals (Sweden)

    Mariya A. Qurieshi


    Full Text Available Cancer is a leading cause of mortality and morbidity in the world. The aim of the present study was to measure the pattern of different cancers in Kashmir, India, a cancer belt with peculiar cancer profile. A hospital based cancer registry was started by the Department of Community Medicine, Government Medical College, Srinagar, in January 2006, wherein information was collected from cancer patients who were diagnosed and treated in the hospital. Data has been analysed for a period extending from January 2006 to December 2012. Descriptive analysis has been done by using statistical software. A total of 1598 cancer patients were admitted during this period. Overall male to female ratio was 1.33 : 1. Stomach cancer was the most commonly reported cancer (25.2%, followed by colorectal cancer (16.4% and lung cancer (13.2% among males. For females, colorectal cancer (16.8%, breast cancer (16.1%, and stomach cancer (10.4% were the most frequently reported cancers in order of frequency. Tobacco related cancers contributed to more than three-fourths of cancers among men and more than half of cancers for women. There is an urgent need to set up a population based cancer registration system to understand the profile of cancers specific to this geographic region.

  14. Molecular cytogenetic applications in analysis of the cancer genome. (United States)

    Rao, Pulivarthi H; Nandula, Subhadra V; Murty, Vundavalli V


    Cancer cells exhibit nonrandom and complex chromosome abnormalities. The role of genomic changes in cancer is well established. However, the identification of complex and cryptic chromosomal changes is beyond the resolution of conventional banding methods. The fluorescence microscopy afforded by imaging technologies, developed recently, facilitates a precise identification of these chromosome alterations in cancer. The three most commonly utilized molecular cytogenetics methods comparative genomic hybridization, spectral karyotype, and fluorescence in situ hybridization, that have already become benchmark tools in cancer cytogenetics, are described in this chapter. Comparative genomic hybridization is a powerful tool for screening copy-number changes in tumor genomes without the need for preparation of metaphases from tumor cells. Multicolor spectral karyotype permits visualization of all chromosomes in one experiment permitting identification of precise chromosomal changes on metaphases derived from tumor cells. The uses of fluorescence in situ hybridization are diverse, including mapping of alteration in single copy genes, chromosomal regions, or entire chromosomes. The opportunities to detect genetic alterations in cancer cells continue to evolve with the use of these methodologies both in diagnosis and research.

  15. Global DNA hypomethylation in peripheral blood leukocytes as a biomarker for cancer risk: a meta-analysis.

    Directory of Open Access Journals (Sweden)

    Hae Dong Woo

    Full Text Available BACKGROUND: Good biomarkers for early detection of cancer lead to better prognosis. However, harvesting tumor tissue is invasive and cannot be routinely performed. Global DNA methylation of peripheral blood leukocyte DNA was evaluated as a biomarker for cancer risk. METHODS: We performed a meta-analysis to estimate overall cancer risk according to global DNA hypomethylation levels among studies with various cancer types and analytical methods used to measure DNA methylation. Studies were systemically searched via PubMed with no language limitation up to July 2011. Summary estimates were calculated using a fixed effects model. RESULTS: The subgroup analyses by experimental methods to determine DNA methylation level were performed due to heterogeneity within the selected studies (p<0.001, I(2: 80%. Heterogeneity was not found in the subgroup of %5-mC (p = 0.393, I(2: 0% and LINE-1 used same target sequence (p = 0.097, I(2: 49%, whereas considerable variance remained in LINE-1 (p<0.001, I(2: 80% and bladder cancer studies (p = 0.016, I(2: 76%. These results suggest that experimental methods used to quantify global DNA methylation levels are important factors in the association study between hypomethylation levels and cancer risk. Overall, cancer risks of the group with the lowest DNA methylation levels were significantly higher compared to the group with the highest methylation levels [OR (95% CI: 1.48 (1.28-1.70]. CONCLUSIONS: Global DNA hypomethylation in peripheral blood leukocytes may be a suitable biomarker for cancer risk. However, the association between global DNA methylation and cancer risk may be different based on experimental methods, and region of DNA targeted for measuring global hypomethylation levels as well as the cancer type. Therefore, it is important to select a precise and accurate surrogate marker for global DNA methylation levels in the association studies between global DNA methylation levels in peripheral

  16. Numerical methods in software and analysis

    CERN Document Server

    Rice, John R


    Numerical Methods, Software, and Analysis, Second Edition introduces science and engineering students to the methods, tools, and ideas of numerical computation. Introductory courses in numerical methods face a fundamental problem-there is too little time to learn too much. This text solves that problem by using high-quality mathematical software. In fact, the objective of the text is to present scientific problem solving using standard mathematical software. This book discusses numerous programs and software packages focusing on the IMSL library (including the PROTRAN system) and ACM Algorithm

  17. Single-cell analysis - Methods and protocols


    Carlo Alberto Redi


    This is certainly a timely volume in the Methods in molecular biology series: we already entered the synthetic biology era and thus we need to be aware of the new methodological advances able to fulfill the new and necessary needs for biologists, biotechnologists and nano-biotechnologists. Notably, among these, the possibility to perform single cell analysis allow researchers to capture single cell responses....

  18. Modern methods of wine quality analysis

    Directory of Open Access Journals (Sweden)

    Галина Зуфарівна Гайда


    Full Text Available  In this paper physical-chemical and enzymatic methods of quantitative analysis of the basic wine components were reviewed. The results of own experiments were presented for the development of enzyme- and cell-based amperometric sensors on ethanol, lactate, glucose, arginine

  19. Systems and methods for sample analysis

    Energy Technology Data Exchange (ETDEWEB)

    Cooks, Robert Graham; Li, Guangtao; Li, Xin; Ouyang, Zheng


    The invention generally relates to systems and methods for sample analysis. In certain embodiments, the invention provides a system for analyzing a sample that includes a probe including a material connected to a high voltage source, a device for generating a heated gas, and a mass analyzer.

  20. Spectroscopic Chemical Analysis Methods and Apparatus (United States)

    Hug, William F. (Inventor); Reid, Ray D. (Inventor); Bhartia, Rohit (Inventor); Lane, Arthur L. (Inventor)


    Spectroscopic chemical analysis methods and apparatus are disclosed which employ deep ultraviolet (e.g. in the 200 nm to 300 nm spectral range) electron beam pumped wide bandgap semiconductor lasers, incoherent wide bandgap semiconductor light emitting devices, and hollow cathode metal ion lasers to perform non-contact, non-invasive detection of unknown chemical analytes. These deep ultraviolet sources enable dramatic size, weight and power consumption reductions of chemical analysis instruments. In some embodiments, Raman spectroscopic detection methods and apparatus use ultra-narrow-band angle tuning filters, acousto-optic tuning filters, and temperature tuned filters to enable ultra-miniature analyzers for chemical identification. In some embodiments Raman analysis is conducted along with photoluminescence spectroscopy (i.e. fluorescence and/or phosphorescence spectroscopy) to provide high levels of sensitivity and specificity in the same instrument.

  1. Multiple predictor smoothing methods for sensitivity analysis.

    Energy Technology Data Exchange (ETDEWEB)

    Helton, Jon Craig; Storlie, Curtis B.


    The use of multiple predictor smoothing methods in sampling-based sensitivity analyses of complex models is investigated. Specifically, sensitivity analysis procedures based on smoothing methods employing the stepwise application of the following nonparametric regression techniques are described: (1) locally weighted regression (LOESS), (2) additive models, (3) projection pursuit regression, and (4) recursive partitioning regression. The indicated procedures are illustrated with both simple test problems and results from a performance assessment for a radioactive waste disposal facility (i.e., the Waste Isolation Pilot Plant). As shown by the example illustrations, the use of smoothing procedures based on nonparametric regression techniques can yield more informative sensitivity analysis results than can be obtained with more traditional sensitivity analysis procedures based on linear regression, rank regression or quadratic regression when nonlinear relationships between model inputs and model predictions are present.

  2. Practical Fourier analysis for multigrid methods

    CERN Document Server

    Wienands, Roman


    Before applying multigrid methods to a project, mathematicians, scientists, and engineers need to answer questions related to the quality of convergence, whether a development will pay out, whether multigrid will work for a particular application, and what the numerical properties are. Practical Fourier Analysis for Multigrid Methods uses a detailed and systematic description of local Fourier k-grid (k=1,2,3) analysis for general systems of partial differential equations to provide a framework that answers these questions.This volume contains software that confirms written statements about convergence and efficiency of algorithms and is easily adapted to new applications. Providing theoretical background and the linkage between theory and practice, the text and software quickly combine learning by reading and learning by doing. The book enables understanding of basic principles of multigrid and local Fourier analysis, and also describes the theory important to those who need to delve deeper into the detai...

  3. Feature extraction techniques using multivariate analysis for identification of lung cancer volatile organic compounds (United States)

    Thriumani, Reena; Zakaria, Ammar; Hashim, Yumi Zuhanis Has-Yun; Helmy, Khaled Mohamed; Omar, Mohammad Iqbal; Jeffree, Amanina; Adom, Abdul Hamid; Shakaff, Ali Yeon Md; Kamarudin, Latifah Munirah


    In this experiment, three different cell cultures (A549, WI38VA13 and MCF7) and blank medium (without cells) as a control were used. The electronic nose (E-Nose) was used to sniff the headspace of cultured cells and the data were recorded. After data pre-processing, two different features were extracted by taking into consideration of both steady state and the transient information. The extracted data are then being processed by multivariate analysis, Linear Discriminant Analysis (LDA) to provide visualization of the clustering vector information in multi-sensor space. The Probabilistic Neural Network (PNN) classifier was used to test the performance of the E-Nose on determining the volatile organic compounds (VOCs) of lung cancer cell line. The LDA data projection was able to differentiate between the lung cancer cell samples and other samples (breast cancer, normal cell and blank medium) effectively. The features extracted from the steady state response reached 100% of classification rate while the transient response with the aid of LDA dimension reduction methods produced 100% classification performance using PNN classifier with a spread value of 0.1. The results also show that E-Nose application is a promising technique to be applied to real patients in further work and the aid of Multivariate Analysis; it is able to be the alternative to the current lung cancer diagnostic methods.

  4. A meta-analysis of serum cancer antigen 125 array for diagnosis of ovarian cancer in Chinese

    Directory of Open Access Journals (Sweden)

    Xiao-Yan Liao


    Full Text Available Objective: To further evaluation the diagnosis accuracy of serum cancer antigen 125 (CA125 in the diagnosis of ovarian cancer in Chinese patients. Materials and Methods: The PubMed, Wanfang and CNKI databases were electric searched and relevant diagnosis trials were reviewed and finally included in this meta-analysis. The diagnosis sensitivity, specificity, positive likely hood ratio (+LR, negative likely hood ratio (−LR, diagnostic odds ratio (DOR and receiver operating characteristic curve were pooled by Meta DiSc 1.4 software. Results: Nineteen studies with a total of 2426 subjects were included in this meta-analysis. The pooled sensitivity, specificity, +LR, −LR and DOR were 0.75 (95% confidence interval = 0.73-0.78, 0.80 (0.77-0.82, 4.52 (3.27-6.26, 0.31 (0.28-0.35 and 15.76 (10.45-23.75 respectively. The area under the summary receiver operating characteristic curve was 0.84. Conclusion: Serum CA125 was potential biomarker for diagnosis of ovarian cancer with acceptable diagnosis value.

  5. A historical discourse analysis of the cancerous and non-cancerous body in secondary biology textbooks (United States)

    Bowers, Neil Thomas

    This dissertation applies the archeological concepts developed by Michel Foucault to a study of thirteen biology textbooks (1993-2004) in order to develop an understanding of 'purchased truths' concerning cancer. This study focuses on the construction of the health/illness dialogue concerning cancer within the textbooks and not the meaning that the individual makes from reading the text; as such this study concerns itself with social truths rather than the search for an individual awareness of names, dates, or places. This study investigates the practices that allow the creation of dialogues that are inserted into a biology textbook and looks at how discursive formations create the 'truth regime' from which the biology textbook is said to speak. Using the Foucaultian themes of 'event', 'emergence', 'enunciation', and 'exteriority' a new reading of topics concerning cancer emerge from biology textbooks. Cancer is a disease that will impact the lives of countless individuals but coverage devoted to the pathology of cancer in secondary biology textbooks is very limited and no study textbook devoted a whole chapter to the discussion of cancer. There is an identified reduction in the number of pages and depth of coverage devoted to cancer in the newer biology texts compared to the older texts. Humans are pictured more than plants or animals in presentations concerning cancer with emphasis being placed on the digitalization of human cells via the scanning electron microscope. When the whole body is presented it is seldom located within the technology of disease diagnosis and treatment but rather is posed for specific social control. Just as each digitized picture of the cancerous cell in the texts is used to create a story so too are the pictures of the whole body in action. Possible story lines offered by the publishing houses concerning the reaction of the body to cancer are shown to intermingle with risk factor analysis to project a sense of Foucaultian

  6. Performance analysis of morphological component analysis (MCA) method for mammograms using some statistical features (United States)

    Gardezi, Syed Jamal Safdar; Faye, Ibrahima; Kamel, Nidal; Eltoukhy, Mohamed Meselhy; Hussain, Muhammad


    Early detection of breast cancer helps reducing the mortality rates. Mammography is very useful tool in breast cancer detection. But it is very difficult to separate different morphological features in mammographic images. In this study, Morphological Component Analysis (MCA) method is used to extract different morphological aspects of mammographic images by effectively preserving the morphological characteristics of regions. MCA decomposes the mammogram into piecewise smooth part and the texture part using the Local Discrete Cosine Transform (LDCT) and Curvelet Transform via wrapping (CURVwrap). In this study, simple comparison in performance has been done using some statistical features for the original image versus the piecewise smooth part obtained from the MCA decomposition. The results show that MCA suppresses the structural noises and blood vessels from the mammogram and enhances the performance for mass detection.

  7. Digital Forensics Analysis of Spectral Estimation Methods

    CERN Document Server

    Mataracioglu, Tolga


    Steganography is the art and science of writing hidden messages in such a way that no one apart from the intended recipient knows of the existence of the message. In today's world, it is widely used in order to secure the information. In this paper, the traditional spectral estimation methods are introduced. The performance analysis of each method is examined by comparing all of the spectral estimation methods. Finally, from utilizing those performance analyses, a brief pros and cons of the spectral estimation methods are given. Also we give a steganography demo by hiding information into a sound signal and manage to pull out the information (i.e, the true frequency of the information signal) from the sound by means of the spectral estimation methods.

  8. An updated meta-analysis of fatal adverse events caused by bevacizumab therapy in cancer patients.

    Directory of Open Access Journals (Sweden)

    Hongxin Huang

    Full Text Available BACKGROUND: The risk of fatal adverse events (FAEs due to bevacizumab-based chemotherapy has not been well described; we carried out an updated meta-analysis regarding this issue. METHODS: An electronic search of Medline, Embase and The Cochrane Central Register of Controlled Trials was conducted to investigate the effects of randomized controlled trials on bevacizumab treatment on cancer patients. Random or fixed-effect meta-analytical models were used to evaluate the risk ratio (RR of FAEs due to the use of bevacizumab. RESULTS: Thirty-four trials were included. Allocation to bevacizumab therapy significantly increased the risk of FAEs; the RR was 1.29 (95% CI:1.05-1.57. This association varied significantly with tumor types (P=0.002 and chemotherapeutic agents (P=0.005 but not with bevacizumab dose (P=0.90. Increased risk was seen in patients with non-small cell lung cancer, pancreatic cancer, prostate cancer, and ovarian cancer. However, FAEs were lower in breast cancer patients treated with bevacizumab. In addition, bevacizumab was associated with an increased risk of FAEs in patients who received concomitant agents of taxanes and/or platinum. CONCLUSION: Compared with chemotherapy alone, the addition of bevacizumab was associated with an increased risk of FAEs among patients with special tumor types, particularly when combined with chemotherapeutic agents such as platinum.

  9. Direct ChromOSOme Analysis and FISH Detection of Primary Gastric cancer

    Institute of Scientific and Technical Information of China (English)


    Objective: To investigate chromosome aberrations and their role in the genesis and development of primary gastric cancer. Methods: An improved, direct chromosome preparation from solid tumors was adopted for G-banding analysis followed by FISH on decolored G-banding chromosomes so that chromosome aberrations could be confirmed at DNA level. Results: A total of 28 primary gastric cancer specimens were studies. Case 1 and case 2 had simple chromosome numerical changes: 49, XY, +2, +8, +9 and 48, +8, +20, respectively. All but case 1 and 2 had complicated chromosome abnormalities. Chromosome structural of frequent occurrence involved del(7q)(21/26), del(3p)(14/26), del(lp)(l1/26) and del(17p)(10/26). The chromosome abnormalities could be simple and complicated. In former, numerical changes involving 1 to 3 chromosome could be observed. Trisomies 8 and 9 might represent a cytogenetic subgroup of primary gastric cancer. In the later, the del(7q) was the most consistent aberration. 7q32-qter was the commonly lost segment. Conclusion: Numerical and structural alterations of chromosomes are present in primary gastric cancer. Del(7q) is one of the structural change characteristic of primary gastric cancer. In the 7q32-qter fragment, a tumor suppressor gene probably exists and it may have close relation to the genesis and progression of gastric cancer.

  10. Metabolic syndrome is associated with increased breast cancer risk: a systematic review with meta-analysis. (United States)

    Bhandari, Ruchi; Kelley, George A; Hartley, Tara A; Rockett, Ian R H


    Background. Although individual metabolic risk factors are reported to be associated with breast cancer risk, controversy surrounds risk of breast cancer from metabolic syndrome (MS). We report the first systematic review and meta-analysis of the association between MS and breast cancer risk in all adult females. Methods. Studies were retrieved by searching four electronic reference databases [PubMed, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Web of Science, and ProQuest through June 30, 2012] and cross-referencing retrieved articles. Eligible for inclusion were longitudinal studies reporting associations between MS and breast cancer risk among females aged 18 years and older. Relative risks and 95% confidence intervals were calculated for each study and pooled using random-effects models. Publication bias was assessed quantitatively (Trim and Fill) and qualitatively (funnel plots). Heterogeneity was examined using Q and I (2) statistics. Results. Representing nine independent cohorts and 97,277 adult females, eight studies met the inclusion criteria. A modest, positive association was observed between MS and breast cancer risk (RR: 1.47, 95% CI, 1.15-1.87; z = 3.13; p = 0.002; Q = 26.28, p = 0.001; I (2) = 69.55%). No publication bias was observed. Conclusions. MS is associated with increased breast cancer risk in adult women.

  11. Metabolic Syndrome Is Associated with Increased Breast Cancer Risk: A Systematic Review with Meta-Analysis

    Directory of Open Access Journals (Sweden)

    Ruchi Bhandari


    Full Text Available Background. Although individual metabolic risk factors are reported to be associated with breast cancer risk, controversy surrounds risk of breast cancer from metabolic syndrome (MS. We report the first systematic review and meta-analysis of the association between MS and breast cancer risk in all adult females. Methods. Studies were retrieved by searching four electronic reference databases [PubMed, Cumulative Index to Nursing and Allied Health Literature (CINAHL, Web of Science, and ProQuest through June 30, 2012] and cross-referencing retrieved articles. Eligible for inclusion were longitudinal studies reporting associations between MS and breast cancer risk among females aged 18 years and older. Relative risks and 95% confidence intervals were calculated for each study and pooled using random-effects models. Publication bias was assessed quantitatively (Trim and Fill and qualitatively (funnel plots. Heterogeneity was examined using Q and I2 statistics. Results. Representing nine independent cohorts and 97,277 adult females, eight studies met the inclusion criteria. A modest, positive association was observed between MS and breast cancer risk (RR: 1.47, 95% CI, 1.15–1.87; z=3.13; p=0.002; Q=26.28, p=0.001; I2=69.55%. No publication bias was observed. Conclusions. MS is associated with increased breast cancer risk in adult women.

  12. Simple gas chromatographic method for furfural analysis. (United States)

    Gaspar, Elvira M S M; Lopes, João F


    A new, simple, gas chromatographic method was developed for the direct analysis of 5-hydroxymethylfurfural (5-HMF), 2-furfural (2-F) and 5-methylfurfural (5-MF) in liquid and water soluble foods, using direct immersion SPME coupled to GC-FID and/or GC-TOF-MS. The fiber (DVB/CAR/PDMS) conditions were optimized: pH effect, temperature, adsorption and desorption times. The method is simple and accurate (RSDTOF-MS: 0.3, 1.2 and 0.9 ngmL(-1) for 2-F, 5-MF and 5-HMF, respectively). It was applied to different commercial food matrices: honey, white, demerara, brown and yellow table sugars, and white and red balsamic vinegars. This one-step, sensitive and direct method for the analysis of furfurals will contribute to characterise and quantify their presence in the human diet.

  13. Heteroscedastic regression analysis method for mixed data

    Institute of Scientific and Technical Information of China (English)

    FU Hui-min; YUE Xiao-rui


    The heteroscedastic regression model was established and the heteroscedastic regression analysis method was presented for mixed data composed of complete data, type- I censored data and type- Ⅱ censored data from the location-scale distribution. The best unbiased estimations of regression coefficients, as well as the confidence limits of the location parameter and scale parameter were given. Furthermore, the point estimations and confidence limits of percentiles were obtained. Thus, the traditional multiple regression analysis method which is only suitable to the complete data from normal distribution can be extended to the cases of heteroscedastic mixed data and the location-scale distribution. So the presented method has a broad range of promising applications.


    Directory of Open Access Journals (Sweden)

    T. D. Tabolinovskaya


    Full Text Available The cryogenic treatment results that have no analogues in Russian and foreign practice were analyzed in 121 patients with tongue cancer. The data on survival rates were used to objectively evaluate the efficiency of tongue cancer cryodestruction in accordance with the extent and pattern of a tumor process. Analysis of long-term (5–30-years results indicated the efficiency of cryodestruction used alone and in combination with radiation and drug therapies in 83.6 % of the new-onset patients and in 73.3 % of the patients with circumscribed recurrences and residual tumors. Recurrent cancer occurred in 19.3 % of 109 patients who had completed treatment: in 16.4 % of the new-onset patients and in 26.7 % of the patients with recurrences and uncured tumors. Local complications from the wound occurred in 6.6 % of the patients and were abolished in the postoperative period.

  15. Immunoexpression analysis and prognostic value of BLCAP in breast cancer

    DEFF Research Database (Denmark)

    Gromova, Irina; Gromov, Pavel; Kroman, Niels;


    patients within the Danish Center for Translational Breast Cancer Research (DCTB) prospective study dataset. The staining pattern, the distribution of the immunostaining, and its intensity were studied in detail. We observed weak immunoreactivity for BLCAP in mammary epithelial cells, almost exclusively......, such as cervical and renal cancer, as well as human tongue carcinoma and osteosarcoma. Here we report the first study of the expression patterns of BLCAP in breast tissue. We analyzed by immunohistochemistry tissue sections of normal and malignant specimens collected from 123 clinical high-risk breast cancer...... localizing to the cytoplasm and found that levels of expression of BLCAP were generally higher in malignant cells as compared to normal cells. Quantitative IHC analysis of BLCAP expression in breast tissues confirmed this differential BLCAP expression in tumor cells, and we could establish, in a 62-patient...

  16. Quantitative DNA methylation analysis of candidate genes in cervical cancer.

    Directory of Open Access Journals (Sweden)

    Erin M Siegel

    Full Text Available Aberrant DNA methylation has been observed in cervical cancer; however, most studies have used non-quantitative approaches to measure DNA methylation. The objective of this study was to quantify methylation within a select panel of genes previously identified as targets for epigenetic silencing in cervical cancer and to identify genes with elevated methylation that can distinguish cancer from normal cervical tissues. We identified 49 women with invasive squamous cell cancer of the cervix and 22 women with normal cytology specimens. Bisulfite-modified genomic DNA was amplified and quantitative pyrosequencing completed for 10 genes (APC, CCNA, CDH1, CDH13, WIF1, TIMP3, DAPK1, RARB, FHIT, and SLIT2. A Methylation Index was calculated as the mean percent methylation across all CpG sites analyzed per gene (~4-9 CpG site per sequence. A binary cut-point was defined at >15% methylation. Sensitivity, specificity and area under ROC curve (AUC of methylation in individual genes or a panel was examined. The median methylation index was significantly higher in cases compared to controls in 8 genes, whereas there was no difference in median methylation for 2 genes. Compared to HPV and age, the combination of DNA methylation level of DAPK1, SLIT2, WIF1 and RARB with HPV and age significantly improved the AUC from 0.79 to 0.99 (95% CI: 0.97-1.00, p-value = 0.003. Pyrosequencing analysis confirmed that several genes are common targets for aberrant methylation in cervical cancer and DNA methylation level of four genes appears to increase specificity to identify cancer compared to HPV detection alone. Alterations in DNA methylation of specific genes in cervical cancers, such as DAPK1, RARB, WIF1, and SLIT2, may also occur early in cervical carcinogenesis and should be evaluated.

  17. Quantitative DNA methylation analysis of candidate genes in cervical cancer. (United States)

    Siegel, Erin M; Riggs, Bridget M; Delmas, Amber L; Koch, Abby; Hakam, Ardeshir; Brown, Kevin D


    Aberrant DNA methylation has been observed in cervical cancer; however, most studies have used non-quantitative approaches to measure DNA methylation. The objective of this study was to quantify methylation within a select panel of genes previously identified as targets for epigenetic silencing in cervical cancer and to identify genes with elevated methylation that can distinguish cancer from normal cervical tissues. We identified 49 women with invasive squamous cell cancer of the cervix and 22 women with normal cytology specimens. Bisulfite-modified genomic DNA was amplified and quantitative pyrosequencing completed for 10 genes (APC, CCNA, CDH1, CDH13, WIF1, TIMP3, DAPK1, RARB, FHIT, and SLIT2). A Methylation Index was calculated as the mean percent methylation across all CpG sites analyzed per gene (~4-9 CpG site) per sequence. A binary cut-point was defined at >15% methylation. Sensitivity, specificity and area under ROC curve (AUC) of methylation in individual genes or a panel was examined. The median methylation index was significantly higher in cases compared to controls in 8 genes, whereas there was no difference in median methylation for 2 genes. Compared to HPV and age, the combination of DNA methylation level of DAPK1, SLIT2, WIF1 and RARB with HPV and age significantly improved the AUC from 0.79 to 0.99 (95% CI: 0.97-1.00, p-value = 0.003). Pyrosequencing analysis confirmed that several genes are common targets for aberrant methylation in cervical cancer and DNA methylation level of four genes appears to increase specificity to identify cancer compared to HPV detection alone. Alterations in DNA methylation of specific genes in cervical cancers, such as DAPK1, RARB, WIF1, and SLIT2, may also occur early in cervical carcinogenesis and should be evaluated.

  18. Increased risk of lung cancer in individuals with a family history of the disease: A pooled analysis from the International Lung Cancer Consortium.

    NARCIS (Netherlands)

    Cote, M.L.; Liu, M.; Bonassi, S.; Neri, M.; Schwartz, A.G.; Christiani, D.C.; Spitz, M.R.; Muscat, J.E.; Rennert, G.; Aben, K.K.H.; Andrew, A.S.; Bencko, V.; Bickeboller, H.; Boffetta, P.; Brennan, P.; Brenner, H.; Duell, E.J.; Fabianova, E.; Field, J.K.; Foretova, L.; Friis, S.; Harris, C.C.; Holcatova, I.; Hong, Y.C.; Isla, D.; Janout, V.; Kiemeney, L.A.L.M.; Kiyohara, C.; Lan, Q.; Lazarus, P.; Lissowska, J.; Marchand, L. le; Mates, D.; Matsuo, K.; Mayordomo, J.I.; McLaughlin, J.R.; Morgenstern, H.; Mueller, H.; Orlow, I.; Park, B.J.; Pinchev, M.; Raji, O.Y.; Rennert, H.S.; Rudnai, P.; Seow, A.; Stucker, I.; Szeszenia-Dabrowska, N.; Teare, M.D.; Tjonnelan, A.; Ugolini, D.; Heijden, E. van der; Wichmann, E.; Wiencke, J.K.; Woll, P.J.; Yang, P.; Zaridze, D.; Zhang, Z.F.; Etzel, C.J.; Hung, R.J.


    BACKGROUND AND METHODS: Familial aggregation of lung cancer exists after accounting for cigarette smoking. However, the extent to which family history affects risk by smoking status, histology, relative type and ethnicity is not well described. This pooled analysis included 24 case-control studies i

  19. Feature Extraction and Analysis of Breast Cancer Specimen (United States)

    Bhattacharyya, Debnath; Robles, Rosslin John; Kim, Tai-Hoon; Bandyopadhyay, Samir Kumar

    In this paper, we propose a method to identify abnormal growth of cells in breast tissue and suggest further pathological test, if necessary. We compare normal breast tissue with malignant invasive breast tissue by a series of image processing steps. Normal ductal epithelial cells and ductal / lobular invasive carcinogenic cells also consider for comparison here in this paper. In fact, features of cancerous breast tissue (invasive) are extracted and analyses with normal breast tissue. We also suggest the breast cancer recognition technique through image processing and prevention by controlling p53 gene mutation to some greater extent.

  20. Association between promoter polymorphisms of OPN gene and cancer risk: a meta-analysis

    Directory of Open Access Journals (Sweden)

    Liu JW


    Full Text Available Jingwei Liu,1–2 Caiyun He,1–2 Quan Yuan,1–2 Zhenning Wang,1–2 Chengzhong Xing,1–2 Yuan Yuan1–2 1Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, 2Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Education Department, Shenyang, People’s Republic of China Background: Results of the association between polymorphisms of osteopontin (OPN gene promoter region and risk of cancer were inconclusive. The aim of this meta-analysis was to elucidate whether OPN promoter polymorphisms were associated with cancer risk.Methods: Electronic databases including PubMed, Web of Science, and Chinese National Knowledge Infrastructure were systematically searched. Odd ratios (ORs and their 95% confidential interval (CI were used to assess the strength of association between OPN promoter polymorphisms and cancer risks.Results: Nine studies were finally included in this meta-analysis. For OPN rs17524488 polymorphism, carriers of GG or -/G genotype were significantly associated with increased cancer risk compared with wild-type -/- carriers, respectively (GG vs -/-: OR =1.40, 95% CI =1.03–1.91, P=0.033; -/G vs -/-: OR =1.22, 95% CI =1.07–1.40, P=0.002. Additionally, G allele was significantly associated with increased cancer risk compared with (- allele (OR =1.21, 95% CI =1.04–1.40, P=0.016. However, no significant association was observed of OPN rs11730582 polymorphism and cancer risk (CC vs TT: OR =0.98, 95% CI =0.49–1.97, P=0.964; CT vs TT: OR =0.88, 95% CI =0.54–1.43, P=0.610.Conclusion: Carriers of GG or -/G genotype of OPN promoter rs17524488 (-156-/G polymorphism might be associated with increased risk of cancer compared with wild-type -/- carriers, respectively. However, no significant association was observed between OPN promoter rs11730582 (-443C/T polymorphism and risk of cancer. Keywords: OPN

  1. Analysis of clinicopathological factors associated with bone metastasis in breast cancer. (United States)

    Chen, Jing; Zhu, Shu; Xie, Xiu-zhen; Guo, Shan-feng; Tong, Liang-qian; Zhou, Sheng; Zhao, Ming; Xianyu, Zhi-qun; Zhu, Xiao-hua; Xiong, Wei


    Breast cancer is the second leading cause of cancer death in women today. Once breast cancer metastasizes to bone, mortality increases. Thus, there is an urgent need to identify patients with high risk of bone metastasis, and to find predictive factors for the occurrence of bone metastasis at an earlier stage of breast cancer. Three hundred and sixty patients with pathologically proved breast cancer visiting the Department of Nuclear Medicine for whole body bone scan from January 2006 and January 2009 were investigated in this study. Clinicopathological information was obtained, which consisted of age, menopausal status, clinical staging, lymph node stage, histological grade, the expression of estrogen receptor (ER), progesterone receptor (PR) and epidermal growth factor receptor 2 (HER2). Correlation between bone metastasis and the associated factors was tested by using the Chi-square test. A Cox multivariate analysis was used to assess the factors which independently contributed to survival after bone metastasis in breast cancer patients. Survival curves were drawn for metastasis-free interval and the independent factors which contributed to survival, using the Kaplan-Meier method. Twenty-four patients were excluded from subsequent analysis. Three hundred and thirty-six enrolled patients ranged in age from 22 to 77 years (mean, 47.8 years). ER/PR status [ER(+) vs. ER(-), χ (2)=4.328, P=0.037; ER(+)PR(+) vs. ER(+)PR(-), χ (2)=4.425, P=0.035] and histological grade (χ (2)=7.131, P=0.028) were significantly associated with bone metastasis. ER status (x (2)=8.315, P=0.004) and metastasis-free interval (χ (2)=6.863, P=0.009) were independent prognostic factors for survival in breast cancer patients with bone metastasis. Our study suggested that ER/PR status and histological grade are risk factors for the development of bone metastasis in breast cancer patients. However, ER status and metastasis-free interval are independent prognostic factors for survival in

  2. Magnetic resonance imaging texture analysis classification of primary breast cancer

    Energy Technology Data Exchange (ETDEWEB)

    Waugh, S.A.; Lerski, R.A. [Ninewells Hospital and Medical School, Department of Medical Physics, Dundee (United Kingdom); Purdie, C.A.; Jordan, L.B. [Ninewells Hospital and Medical School, Department of Pathology, Dundee (United Kingdom); Vinnicombe, S. [University of Dundee, Division of Imaging and Technology, Ninewells Hospital and Medical School, Dundee (United Kingdom); Martin, P. [Ninewells Hospital and Medical School, Department of Clinical Radiology, Dundee (United Kingdom); Thompson, A.M. [University of Texas MD Anderson Cancer Center, Department of Surgical Oncology, Houston, TX (United States)


    Patient-tailored treatments for breast cancer are based on histological and immunohistochemical (IHC) subtypes. Magnetic Resonance Imaging (MRI) texture analysis (TA) may be useful in non-invasive lesion subtype classification. Women with newly diagnosed primary breast cancer underwent pre-treatment dynamic contrast-enhanced breast MRI. TA was performed using co-occurrence matrix (COM) features, by creating a model on retrospective training data, then prospectively applying to a test set. Analyses were blinded to breast pathology. Subtype classifications were performed using a cross-validated k-nearest-neighbour (k = 3) technique, with accuracy relative to pathology assessed and receiver operator curve (AUROC) calculated. Mann-Whitney U and Kruskal-Wallis tests were used to assess raw entropy feature values. Histological subtype classifications were similar across training (n = 148 cancers) and test sets (n = 73 lesions) using all COM features (training: 75 %, AUROC = 0.816; test: 72.5 %, AUROC = 0.823). Entropy features were significantly different between lobular and ductal cancers (p < 0.001; Mann-Whitney U). IHC classifications using COM features were also similar for training and test data (training: 57.2 %, AUROC = 0.754; test: 57.0 %, AUROC = 0.750). Hormone receptor positive and negative cancers demonstrated significantly different entropy features. Entropy features alone were unable to create a robust classification model. Textural differences on contrast-enhanced MR images may reflect underlying lesion subtypes, which merits testing against treatment response. (orig.)

  3. Analysis of clinical characteristics of 950 cases of cervical cancer

    Directory of Open Access Journals (Sweden)

    Shu-li ZHU


    Full Text Available Objective To discuss the clinical features of the patients suffering from cervical cancer who visited Daping Hospital affiliated to Third Military Medical University in recent 10 years. Methods The clinical data of the patients who were pathologically diagnosed as invasive cervical cancer in Daping Hospital of TMMU from Jan. 2004 to Dec. 2013 were retrospectively analyzed. They were divided into different age groups and analyzed according to age, clinical features, pathological type, and surgical approach. Results Clinical data of 950 patients with invasive cervical cancer were reviewed in this study. The mean age of the patients was 46.9 years. The clinical features, pathological type, and surgical approaches were different in different age groups. Analysis of the age structure of the patients, the onset age of cervical cancer seemed to increase year by year. Conclusion The clinical features of cervical cancer are diversity in different age, and the strategy for controlling its development should be varied according to age. DOI: 10.11855/j.issn.0577-7402.2015.03.09

  4. Ovarian Cancer Screening Method Fails to Reduce Deaths from the Disease | Division of Cancer Prevention (United States)

    New results from the NCI-sponsored Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial show that screening for ovarian cancer with transvaginal ultrasound (TVU) and the CA-125 blood test did not result in fewer deaths from the disease compared with usual care. |

  5. Establishment of a PCR analysis method for canine BRCA2

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    Yoshikawa Yasunaga


    Full Text Available Abstract Background Mammary tumors are the most common tumor type in both human and canine females. In women, carriers of mutations in BRCA2, a tumor suppressor gene product, have a higher risk of breast cancer. Canine BRCA2 has also been suggested to have a relationship with mammary tumors. However, clearly deleterious BRCA2 mutations have not been identified in any canine mammary tumors, as appropriate methods to detect mutations or a consensus BRCA2 sequence have not been reported. Findings For amplification and sequencing of BRCA2, we designed 14 and 20 PCR primer sets corresponding to the BRCA2 open reading frame (ORF and all 27 exons, respectively, including exon-intron boundaries of the canine BRCA2 regions, respectively. To define the consensus canine BRCA2 ORF sequence, we used established methods to sequence the full-length canine BRCA2 ORF sequence from two ovaries and a testis obtained from individual healthy mongrel dogs and partially sequence BRCA2 genomic sequences in 20-56 tumor-free dogs, each aged over 6 years. Subsequently, we compared these sequences and seven previously reported sequences, and defined the most common base sequences as the consensus canine BRCA2 ORF sequence. Moreover, we established a detection method for identifying splicing variants. Unexpectedly, we also identified novel splicing variants in normal testes during establishment of these methods. Conclusions The present analysis methods for determining the BRCA2 base sequence and for detecting BRCA2 splicing variants and the BRCA2 ORF consensus sequence are useful for better understanding the relationship between canine BRCA2 mutation status and cancer risk.

  6. A Healthy Dietary Pattern Reduces Lung Cancer Risk: A Systematic Review and Meta-Analysis

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    Yanlai Sun


    Full Text Available Background: Diet and nutrients play an important role in cancer development and progress; a healthy dietary pattern has been found to be associated with several types of cancer. However, the association between a healthy eating pattern and lung cancer risk is still unclear. Objective: Therefore, we conducted a systematic review with meta-analysis to evaluate whether a healthy eating pattern might reduce lung cancer risk. Methods: We identified relevant studies from the PubMed and Embase databases up to October 2015, and the relative risks were extracted and combined by the fixed-effects model when no substantial heterogeneity was observed; otherwise, the random-effects model was employed. Subgroup and publication bias analyses were also performed. Results: Finally, eight observational studies were included in the meta-analysis. The pooled relative risk of lung cancer for the highest vs. lowest category of healthy dietary pattern was 0.81 (95% confidence interval, CI: 0.75–0.86, and no significant heterogeneity was detected. The relative risks (RRs for non-smokers, former smokers and current smokers were 0.89 (95% CI: 0.63–1.27, 0.74 (95% CI: 0.62–0.89 and 0.86 (95% CI: 0.79–0.93, respectively. The results remained stable in subgroup analyses by other confounders and sensitivity analysis. Conclusions: The results of our meta-analysis suggest that a healthy dietary pattern is associated with a lower lung cancer risk, and they provide more beneficial evidence for changing the diet pattern in the general population.

  7. Screening for candidate genes related to breast cancer with cDNA microarray analysis

    Institute of Scientific and Technical Information of China (English)

    Yu-Juan Xiang; Zhi-Gang Yu; Ming-Ming Guo; Qin-Ye Fu; Zhong-Bing Ma; De-Zong Gao; Qiang Zhang; Yu-Yang Li; Liang Li; Lu Liu; Chun-Miao Ye


    Objective: The aim of this study was to reveal the exact changes during the occurrence of breast cancer to explore significant new and promising genes or factors related to this disease. Methods: We compared the gene expression profiles of breast cancer tissues with its uninvolved normal breast tissues as controls using the cDNA microarray analysis in seven breast cancer patients. Further, one representative gene, named IFI30, was quanti-tatively analyzed by real-time PCR to confirm the result of the cDNA microarray analysis. Results: A total of 427 genes were identified with significantly differential expression, 221 genes were up-regulated and 206 genes were down-regulated. And the result of cDNA microarray analysis was validated by detection of IFI30 mRNA level changes by real-time PCR. Genes for cell proliferation, cell cycle, cell division, mitosis, apoptosis, and immune response were enriched in the up-regulated genes, while genes for cell adhesion, proteolysis, and transport were significantly enriched in the down-regulated genes in breast cancer tissues compared with normal breast tissues by a gene ontology analysis. Conclusion: Our present study revealed a range of differentially expressed genes between breast cancer tissues and normal breast tissues, and provide candidate genes for further study focusing on the pathogenesis and new biomarkers for breast cancer. Copyright © 2015, Chinese Medical Association Production. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NC-ND license (

  8. Vitamin D receptor gene polymorphisms and colorectal cancer risk: A systematic meta-analysis

    Institute of Scientific and Technical Information of China (English)

    Yong-Heng Bai; Hong Lu; Dan Hong; Cheng-Cheng Lin; Zhen Yu; Bi-Cheng Chen


    AIM:To investigate the relationship between polymorphisms present in the vitamin D receptor (VDR) gene and colorectal cancer risk,a systematic meta-analysis of population-based studies was performed.METHODS:A total of 38 relevant reports published between January 1990 and August 2010 were identified,of which only 23 qualified for this meta-analysis based on our selection criteria.Five polymorphic variants of the VDR gene,including Cdx-2 (intron 1e) and FokI (exon 2) present in the 5' region of the gene,and BsmI (intron 8),ApaI (intron 8),and TaqI (exon 9) sites present in the 3' untranslated region (UTR),were evaluated for possible associations with colorectalcancer risk.Review manager 4.2 was used to perform statistical analyses.RESULTS:In the meta-analysis performed,only the BsmI polymorphism was found to be associated with colorectal cancer risk.In particular,the BsmI B genotype was found to be related to an overall decrease in the risk for colorectal cancer [BB vs bb:odds ratio (OR) =0.87,95% CI:0.80-0.94,P =3 x 10-4; BB vs Bb + bb:OR =0.90,95% CI:0.84-0.97,P =5 x 10-4].Moreover,in subgroup analyses,the BsmI B genotype was significantly associated with colon cancer,and not rectal cancer.An absence of between-study heterogeneity was also observed.CONCLUSION:A meta-analysis of 23 published studies identified the BsmI polymorphism of the VDR gene to be associated with an increased risk of colon cancer.

  9. Meta-analysis of association between GSTM1 gene polymorphism and cervical cancer

    Institute of Scientific and Technical Information of China (English)

    Ying Liu; Liang-Zhi Xu


    Objective:To investigate association between glutathione S-transferases (GSTs) and cervical cancer.Methods:Published literature from PubMed, EMBASE, and other databases were retrieved. All studies evaluating the association betweenGSTM1/GSTT1 polymorphisms and cervical were included. Pooled odds ratio (OR) and95% confidence interval (CI) were calculated using fixed- or random-effects model.Results:A total of15 case-control studies were included in the meta-analysis of GSTM1 genotypes (1 825 cases and2 104 controls). The overall result showed that the association betweenGSTM1 null genotype and risk for cervical cancer was statistically significant (OR=1.53, 95%CI=1.18-2.00). Great heterogeneity was found between studies. Subgroup analysises were performed based on smoking and ethnicity. Our results showed that smokers with nullGSTM1 genotype had higher risk of cervical cancer (OR=1.56,95%CI=1.01-2.41). For the ethnicity stratification, significant increased risk of nullGSTM1 genotype was found in Chinese and Indian population, but no increased risk in other population.Conclusions:This meta-analysis provides strong evidence that theGSTM1 null genotype is associated with the development of cervical cancer, and especially in Chinese and Indian population, and smoking shows a modification on the association between GSTM1 null genotype and cervical cancer.

  10. NMD Microarray Analysis for Rapid Genome-Wide Screen of Mutated Genes in Cancer

    Directory of Open Access Journals (Sweden)

    Maija Wolf


    Full Text Available Gene mutations play a critical role in cancer development and progression, and their identification offers possibilities for accurate diagnostics and therapeutic targeting. Finding genes undergoing mutations is challenging and slow, even in the post-genomic era. A new approach was recently developed by Noensie and Dietz to prioritize and focus the search, making use of nonsense-mediated mRNA decay (NMD inhibition and microarray analysis (NMD microarrays in the identification of transcripts containing nonsense mutations. We combined NMD microarrays with array-based CGH (comparative genomic hybridization in order to identify inactivation of tumor suppressor genes in cancer. Such a “mutatomics” screening of prostate cancer cell lines led to the identification of inactivating mutations in the EPHB2 gene. Up to 8% of metastatic uncultured prostate cancers also showed mutations of this gene whose loss of function may confer loss of tissue architecture. NMD microarray analysis could turn out to be a powerful research method to identify novel mutated genes in cancer cell lines, providing targets that could then be further investigated for their clinical relevance and therapeutic potential.

  11. Cancer risk in older people receiving statin therapy: a meta-analysis of randomized controlled trials (United States)

    Liu, Hong-Wei; Bian, Su-Yan; Zhu, Qi-Wei; Zhao, Yue-Xiang


    Background Although statins are well tolerated by most aged people, their potential carcinogenicity is considered as one of the biggest factors limiting the use of statins. The aim of the present study was to determine the risk of cancer in people aged over 60 years receiving statin therapy. Methods A comprehensive search for articles published up to December 2015 was performed, reviews of each randomized controlled trials (RCTs) that compared the effects of statin mono-therapy with placebo on the risk of cancer in people aged > 60 years were conducted and data abstracted. All the included studies were evaluated for publication bias and heterogeneity. Pooled odds ratios (OR) estimates and 95% confidence intervals (CIs) were calculated using the random effects model. Results A total of 12 RCTs, involving 62,927 patients (31,517 in statin therapy group and 31,410 in control group), with a follow-up duration of 1.9–5.4 years, contributed to the analysis. The statin therapy did not affect the overall incidence of cancer (OR = 1.03, 95% CI: 0.94–1.14, P = 0.52); subgroup analyses showed that neither the variety nor the chemical properties of the statins accounted for the incidence of cancer in older people. Conclusions Our meta-analysis findings do not support a potential cancer risk of statin treatment in people over 60 years old. Further targeted researches with a longer follow-up duration are warranted to confirm this issue.

  12. Analysis of human cancer prostate tissues using FTIR microspectroscopy and SRIXE techniques (United States)

    Paluszkiewicz, Czesława; Kwiatek, Wojciech M.


    It is known that Fourier transform infrared (FTIR) spectra of human tissues are specific and can be used to discriminate between various disease states. In this study, cancer and healthy parts of prostate tissues were examined. The human prostate tissues were obtained during surgical operation. Sections of samples were mounted onto Mylar foils and measured by both FTIR microspectroscopy and synchrotron radiation induced X-ray emission (SRIXE) methods. Neighboring sections of tissues analyzed by FTIR and SRIXE were also examined by a histopathologist. Since the SRIXE technique is suitable for trace element analysis the two-dimensional scans on both cancerous and non-cancerous parts of the prostate tissues were done in order to find elemental distribution of trace elements. The single point analysis on selected areas were also performed. Then the same samples were studied in the mid infrared region on Excalibur spectrometer with infrared microscope UMA-500 equipped with an automatic xy-stage and video camera. Both FTIR spectra and elemental distribution show differences between cancerous and non-cancerous parts of the analyzed tissues.

  13. Statin as a Combined Therapy for Advanced-Stage Ovarian Cancer: A Propensity Score Matched Analysis

    Directory of Open Access Journals (Sweden)

    Hong-Yu Chen


    Full Text Available Background. Despite the great achievements in the treatment of advanced-stage ovarian cancer, it is still a severe condition with an unfavorable 5-year survival rate. Statins have been suggested to reduce the risk of several cancers beyond their cholesterol-lowing effects. However, the prognostic significance of statins in patients with advanced-stage ovarian cancer remains controversial. Methods. A retrospective study was performed to evaluate the association between statin intake and overall survival (OS among patients with advanced-stage ovarian cancer. Patients who underwent cytoreductive surgery followed by courses of intravenous chemotherapy were matched through a propensity score analysis. Results. A total of 60 propensity-matched patients were included. Women in statin group showed a similar OS than the nonstatin counterparts (P=0.966, whereas residual tumor was significantly associated with better OS (P=0.013 and was an independent factor that associated with OS (P=0.002, hazard ratio = 5.460, and 95% confidence interval: 1.894 to 15.742 in multivariable analysis. Conclusions. Our results suggested that statin usage was not associated with improved OS in patients with advanced-stage ovarian cancer undergoing surgery and chemotherapy. Considering the retrospective nature and the relative small sample size of the study, further prospective studies and random control trials are needed.

  14. The association between polycystic ovary syndrome and breast cancer: a meta-analysis (United States)

    Shobeiri, Fatemeh


    Objective The results of epidemiological studies investigated the association between polycystic ovary syndrome (PCOS) and the breast cancer are inconsistent. This meta-analysis was conducted to estimate the association between PCOS and the breast cancer risk. We searched PubMed, Web of Science, and Scopus for observational studies until June 2015. Data were independently extracted and analyzed using 95% odds ratio, and confidence intervals (CIs) based on the random-effects models. Methods We identified 970 references and conducted eight studies with 45,470 participants and 243,064 person- year. Results The association between PCOS and the breast cancer risk in case-control studies 0.87 (95% CI, 0.44 to 1.31) and that of cohort studies was estimated 1.18 (95% CI, 0.93 to 1.43). Conclusion This meta-analysis demonstrated that PCOS no does increase the risk of breast cancer. Further prospective cohort studies are needed to provide convincing evidence in order to PCOS can increase or not effect on the risk of the breast cancer. PMID:27668199

  15. CD147 and Prostate Cancer: A Systematic Review and Meta-Analysis (United States)

    Ning, Zhaoze; Yang, Zhenyu; Li, Hongru; Wang, Yonggang; Chen, Fang


    Background Prostate cancer is one of the most common non-cutaneous malignancies in men. We aimed to systemically evaluate the relationship between the expression of CD147 in tissues and the clinicopathological features of prostate cancer. Methods and Findings PubMed (1966–2016), EMBASE (1980–2016), the Cochrane Library (1996–2016), Web of Science (1945–2016), China National Knowledge Infrastructure (1982–2016), and the WanFang databases (1988–2016) were searched. Literature quality assessment was performed with the Newcastle-Ottawa Scale. Meta-analysis was performed by using Review Manager 5.3 and Stata 13.0. A total of 12591 prostate cancer patients from 14 studies were included. The results of the meta-analysis showed that there were significant differences in the positive expression rate in the following comparisons: prostatic cancer tissues vs. normal prostate tissues (odds ratio [OR] = 26.93, 95% confidence interval [CI] 7.95–91.20, P CD147 positive expression rate was closely related to the clinical characteristics of prostate cancer, but more research is needed to confirm the findings owing to the results of the subgroups. PMID:27684938

  16. A Cross-Cancer Genetic Association Analysis of the DNA repair and DNA Damage Signaling Pathways for Lung, Ovary, Prostate, Breast and Colorectal Cancer (United States)

    Scarbrough, Peter M.; Weber, Rachel Palmieri; Iversen, Edwin S.; Brhane, Yonathan; Amos, Christopher I.; Kraft, Peter; Hung, Rayjean J.; Sellers, Thomas A.; Witte, John S.; Pharoah, Paul; Henderson, Brian E.; Gruber, Stephen B.; Hunter, David J.; Garber, Judy E.; Joshi, Amit D.; McDonnell, Kevin; Easton, Doug F.; Eeles, Ros; Kote-Jarai, Zsofia; Muir, Kenneth; Doherty, Jennifer A.; Schildkraut, Joellen M.


    Background DNA damage is an established mediator of carcinogenesis, though GWAS have identified few significant loci. This cross-cancer site, pooled analysis was performed to increase the power to detect common variants of DNA repair genes associated with cancer susceptibility. Methods We conducted a cross-cancer analysis of 60,297 SNPs, at 229 DNA repair gene regions, using data from the NCI Genetic Associations and Mechanisms in Oncology (GAME-ON) Network. Our analysis included data from 32 GWAS and 48,734 controls and 51,537 cases across five cancer sites (breast, colon, lung, ovary, and prostate). Because of the unavailability of individual data, data were analyzed at the aggregate level. Meta-analysis was performed using the Association analysis for SubSETs (ASSET) software. To test for genetic associations that might escape individual variant testing due to small effect sizes, pathway analysis of eight DNA repair pathways was performed using hierarchical modeling. Results We identified three susceptibility DNA repair genes, RAD51B (p < 5.09 × 10−6), MSH5 (p < 5.09 × 10−6) and BRCA2 (p = 5.70 × 10−6). Hierarchical modeling identified several pleiotropic associations with cancer risk in the base excision repair, nucleotide excision repair, mismatch repair, and homologous recombination pathways. Conclusions Only three susceptibility loci were identified which had all been previously reported. In contrast, hierarchical modeling identified several pleiotropic cancer risk associations in key DNA repair pathways. Impact Results suggest that many common variants in DNA repair genes are likely associated with cancer susceptibility through small effect sizes that do not meet stringent significance testing criteria. PMID:26637267

  17. A novel method for monitoring high-risk breast cancer with tumor markers

    DEFF Research Database (Denmark)

    Sölétormos, G; Nielsen, D; Schiøler, V;


    cancer. METHODS: Ninety females with high-risk breast cancer were included in the study. Response evaluation was based upon clinical examination, x-rays or histology and elaborated marker criteria. RESULTS: During the marker monitoring period, metastases in four patients were confined to skin or lymph...

  18. Anti-cancer agents based on 6-trifluoromethoxybenzimidazole derivatives and method of making (United States)

    Gakh, Andrei A; Vovk, Mykhaylo V; Mel& #x27; nychenko, Nina V; Sukach, Volodymyr A


    The present disclosure relates to novel compounds having the structural Formulas (1a,1b), stereoisomers, tautomers, racemics, prodrugs, metabolites thereof, or pharmaceutically acceptable salt and/or solvate thereof as chemotherapy agents for treating of cancer, particularly androgen-independent prostate cancer. The disclosure also relates to methods for preparing said compounds, and to pharmaceutical compositions comprising said compounds.

  19. New methods in mammary gland development and cancer: proteomics, epigenetics, symmetric division and metastasis


    Bentires-Alj, Mohamed; Glukhova, Marina; Hynes, Nancy; Vivanco, Maria dM.


    The European Network for Breast Development and Cancer (ENBDC) meeting on 'Methods in Mammary Gland Development and Cancer' has become an annual international rendezvous for scientists with interests in the normal and neoplastic breast. The fourth meeting in this series, held in April in Weggis, Switzerland, focused on proteomics, epigenetics, symmetric division, and metastasis.

  20. Anti-cancer agents based on 6-trifluoromethoxybenzimidazole derivatives and method of making (United States)

    Gakh, Andrei A.; Vovk, Mykhaylo V.; Mel'nychenko, Nina V.; Sukach, Volodymyr A.


    The present disclosure relates to novel compounds having the structural Formulas (1a,1b), stereoisomers, tautomers, racemics, prodrugs, metabolites thereof, or pharmaceutically acceptable salt and/or solvate thereof as chemotherapy agents for treating of cancer, particularly androgen-independent prostate cancer. The disclosure also relates to methods for preparing said compounds, and to pharmaceutical compositions comprising said compounds.

  1. Meta-analysis of cancer transcriptomes: A new approach to uncover molecular pathological events in different cancer tissues

    Directory of Open Access Journals (Sweden)

    Sundus Iqbal


    Full Text Available To explore secrets of metastatic cancers, individual expression of true sets of respective genes must spread across the tissue. In this study, meta-analysis for transcriptional profiles of oncogenes was carried out to hunt critical genes or networks helping in metastasizing cancers. For this, transcriptomic analysis of different cancerous tissues causing leukemia, lung, liver, spleen, colorectal, colon, breast, bladder, and kidney cancers was performed by extracting microarray expression data from online resource; Gene Expression Omnibus. A newly developed bioinformatics technique; Dynamic Impact Approach (DIA was applied for enrichment analysis of transcriptional profiles using Database for Annotation Visualization and Integrated Discovery (DAVID. Furthermore, oPOSSUM (v. 2.0 and Cytoscape (v. 2.8.2 were used for in-depth analysis of transcription factors and regulatory gene networks respectively. DAVID analysis uncovered the most significantly enriched pathways in molecular functions that were 'Ubiquitin thiolesterase activity' up regulated in blood, breast, bladder, colorectal, lung, spleen, prostrate cancer. 'Transforming growth factor beta receptor activity' was inhibited in all cancers except leukemia, colon and liver cancer. oPOSSUM further revealed highly over-represented Transcription Factors (TFs; Broad-complex_3, Broad-complex_4, and Foxd3 except for leukemia and bladder cancer. From these findings, it is possible to target genes and networks, play a crucial role in the development of cancer. In the future, these transcription factors can serve as potential candidates for the therapeutic drug targets which can impede the deadly spread.

  2. Methods for genetic linkage analysis using trisomies

    Energy Technology Data Exchange (ETDEWEB)

    Feingold, E.; Lamb, N.E.; Sherman, S.L. [Emory Univ., Atlanta, GA (United States)


    Certain genetic disorders (e.g. congenital cataracts, duodenal atresia) are rare in the general population, but more common in people with Down`s syndrome. We present a method for using individuals with trisomy 21 to map genes for such traits. Our methods are analogous to methods for mapping autosomal dominant traits using affected relative pairs by looking for markers with greater than expected identity-by-descent. In the trisomy case, one would take trisomic individuals and look for markers with greater than expected reduction to homozygosity in the chromosomes inherited form the non-disjoining parent. We present statistical methods for performing such a linkage analysis, including a test for linkage to a marker, a method for estimating the distance from the marker to the gene, a confidence interval for that distance, and methods for computing power and sample sizes. The methods are described in the context of gene-dosage model for the etiology of the disorder, but can be extended to other models. We also resolve some practical issues involved in implementing the methods, including how to use partially informative markers, how to test candidate genes, and how to handle the effect of reduced recombination associated with maternal meiosis I non-disjunction.

  3. Dependency in elderly people newly diagnosed with cancer - A mixed-method study

    DEFF Research Database (Denmark)

    Esbensen, Bente Appel; Thomé, Bibbi; Thomsen, Thordis


    PURPOSE: This study, based on data from an empirical investigation, combines quantitative and qualitative approaches in a mixed-method design to explore dependency in elderly people newly diagnosed with cancer. METHODS AND SAMPLE: 101 elderly people newly diagnosed with cancer were included...... be achieved by assessing, Activities of Daily Living (ADL) in the elderly. Receiving assistance from children seems to increase perceived dependency and to affect QoL negatively. CONCLUSIONS: The results of this mixed-method study indicate that dependency had a negative influence on the elderly with cancer...

  4. Method of thermal derivative gradient analysis (TDGA

    Directory of Open Access Journals (Sweden)

    M. Cholewa


    Full Text Available In this work a concept of thermal analysis was shown, using for crystallization kinetics description the temperature derivatives after time and direction. Method of thermal derivative gradient analysis (TDGA is assigned for alloys and metals investigation as well as cast composites in range of solidification. The construction and operation characteristics were presented for the test stand including processing modules and probes together with thermocouples location. Authors presented examples of results interpretation for AlSi11 alloy castings with diversified wall thickness and at different pouring temperature.

  5. Cancer research in need of a scientific revolution: Using 'paradigm shift' as a method of investigation. (United States)

    Wion, Didier; Appaix, Florence; Burruss, Meriwether; Berger, Francois; van der Sanden, Boudewijn


    Despite important human and financial resources and considerable accumulation of scientific publications, patents, and clinical trials, cancer research has been slow in achieving a therapeutic revolution similar to the one that occurred in the last century for infectious diseases. It has been proposed that science proceeds not only by accumulating data but also through paradigm shifts. Here, we propose to use the concept of 'paradigm shift' as a method of investigation when dominant paradigms fail to achieve their promises. The first step in using the 'paradigm shift' method in cancer research requires identifying its founding paradigms. In this review, two of these founding paradigms will be discussed: (i) the reification of cancer as a tumour mass and (ii) the translation of the concepts issued from infectious disease in cancer research. We show how these founding paradigms can generate biases that lead to over-diagnosis and over-treatment and also hamper the development of curative cancer therapies. We apply the 'paradigm shift' method to produce perspective reversals consistent with current experimental evidence. The 'paradigm shift' method enlightens the existence of a tumour physiologic-prophylactic-pathologic continuum. It integrates the target/antitarget concept and that cancer is also an extracellular disease. The 'paradigm shift' method has immediate implications for cancer prevention and therapy. It could be a general method of investigation for other diseases awaiting therapy.

  6. Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Zhe; Wu, Chaochao; Xie, Fang; Slysz, Gordon W.; Tolic, Nikola; Monroe, Matthew E.; Petyuk, Vladislav A.; Payne, Samuel H.; Fujimoto, Grant M.; Moore, Ronald J.; Fillmore, Thomas L.; Schepmoes, Athena A.; Levine, Douglas; Townsend, Reid; Davies, Sherri; Li, Shunqiang; Ellis, Matthew; Boja, Emily; Rivers, Robert; Rodriguez, Henry; Rodland, Karin D.; Liu, Tao; Smith, Richard D.


    Aberrant degradation of proteins is associated with many pathological states, including cancers. Mass spectrometric analysis of tumor peptidomes, the intracellular and intercellular products of protein degradation, has the potential to provide biological insights on proteolytic processing in cancer. However, attempts to use the information on these smaller protein degradation products from tumors for biomarker discovery and cancer biology studies have been fairly limited to date, largely due to the lack of effective approaches for robust peptidomics identification and quantification, and the prevalence of confounding factors and biases associated with sample handling and processing. Herein, we have developed an effective and robust analytical platform for comprehensive analyses of tissue peptidomes, which is suitable for high throughput quantitative studies. The reproducibility and coverage of the platform, as well as the suitability of clinical ovarian tumor and patient-derived breast tumor xenograft samples with post-excision delay of up to 60 min before freezing for peptidomics analysis, have been demonstrated. Moreover, our data also show that the peptidomics profiles can effectively separate breast cancer subtypes, reflecting tumor-associated protease activities. Peptidomics complements results obtainable from conventional bottom-up proteomics, and provides insights not readily obtainable from such approaches.


    Institute of Scientific and Technical Information of China (English)

    LI Jinghua


    Over the past two decades,structural decomposition analysis(SDA)has developed into a major analytical tool in the field of input-output(IO)techniques,but the method was found to suffer from one or more of the following problems.The decomposition forms,which are used to measure the contribution of a specific determinant,are not unique due to the existence of a multitude of equivalent forms,irrational due to the weights of different determinants not matching,inexact due to the existence of large interaction terms.In this paper,a decomposition method is derived to overcome these deficiencies,and we prove that the result of this approach is equal to the Shapley value in cooperative games,and so some properties of the method are obtained.Beyond that,the two approaches that have been used predominantly in the literature have been proved to be the approximate solutions of the method.

  8. Coffee consumption and risk of cancers: a meta-analysis of cohort studies

    Directory of Open Access Journals (Sweden)

    Zou Jian


    Full Text Available Abstract Background Coffee consumption has been shown to be associated with cancer of various sites in epidemiological studies. However, there is no comprehensive overview of the substantial body of epidemiologic evidence. Methods We searched MEDLINE, EMBASE, Science Citation Index Expanded and bibliographies of retrieved articles. Prospective cohort studies were included if they reported relative risks (RRs and corresponding 95% confidence intervals (CIs of various cancers with respect to frequency of coffee intake. We did random-effects meta-analyses and meta-regressions of study-specific incremental estimates to determine the risk of cancer associated with 1 cup/day increment of coffee consumption. Results 59 studies, consisting of 40 independent cohorts, met the inclusion criteria. Compared with individuals who did not or seldom drink coffee per day, the pooled RR of cancer was 0.87 (95% CI, 0.82-0.92 for regular coffee drinkers, 0.89 (0.84-0.93 for low to moderate coffee drinkers, and 0.82 (0.74-0.89 for high drinkers. Overall, an increase in consumption of 1 cup of coffee per day was associated with a 3% reduced risk of cancers (RR, 0.97; 95% CI, 0.96-0.98. In subgroup analyses, we noted that, coffee drinking was associated with a reduced risk of bladder, breast, buccal and pharyngeal, colorectal, endometrial, esophageal, hepatocellular, leukemic, pancreatic, and prostate cancers. Conclusions Findings from this meta-analysis suggest that coffee consumption may reduce the total cancer incidence and it also has an inverse association with some type of cancers.

  9. Spatio-temporal analysis of female breast cancer incidence in Shenzhen, 2007-2012

    Institute of Scientific and Technical Information of China (English)

    Hai-Bin Zhou; Sheng-Yuan Liu; Lin Lei; Zhong-Wei Chen; Ji Peng; Ying-Zhou Yang; Xiao-Li Liu


    Introduction:Breast cancer is a leading tumor with a high mortality in women. This study examined the spatio-temporal distribution of the incidence of female breast cancer in Shenzhen between 2007 and 2012. Methods:The data on breast cancer incidence were obtained from the Shenzhen Cancer Registry System. To describe the temporal trend, the average annual percentage change (AAPC) was analyzed using a joinpoint regression model. Spatial autocorrelation and a retrospective spatio-temporal scan approach were used to detect the spatio-temporal cluster distribution of breast cancer cases. Results:Breast cancer ranked first among different types of cancer in women in Shenzhen between 2007 and 2012 with a crude incidence of 20.0/100,000 population. The age-standardized rate according to the world standard population was 21.1/100,000 in 2012, with an AAPC of 11.3%. The spatial autocorrelation analysis showed a spatial correlation characterized by the presence of a hotspot in south-central Shenzhen, which included the eastern part of Luohu District (Donghu and Liantang Streets) and Yantian District (Shatoujiao, Haishan, and Yantian Streets). Five spatio-temporal cluster areas were detected between 2010 and 2012, one of which was a Class 1 cluster located in southwestern Shenzhen in 2010, which included Yuehai, Nantou, Shahe, Shekou, and Nanshan Streets in Nanshan District with an incidence of 54.1/100,000 and a relative risk of 2.41;the other four were Class 2 clusters located in Yantian, Luohu, Futian, and Longhua Districts with a relative risk ranging from 1.70 to 3.25. Conclusions:This study revealed the spatio-temporal cluster pattern for the incidence of female breast cancer in Shenzhen, which will be useful for a better allocation of health resources in Shenzhen.

  10. Thin-walled Cystic Lung Cancer: An Analysis of 24 Cases and Review of Literatures

    Directory of Open Access Journals (Sweden)

    Juntang GUO


    Full Text Available Background and objective Lung cancer presenting as cystic lesions was first described by Anderson and Pierce in 1954. Lung cancer presenting as cysts is a rare entity in clinical practice. Differential diagnosis is difficult in the benign-like cyst. This study investigated the clinical characteristics, diagnosis and treatment of lung cancer presenting as cysts. Methods We conducted a retrospective analysis of the clinical records of 24 patients who underwent surgery for a primary lung cancer presenting as cysts in our department between 2007 and 2013. We defined a ‘Thin-walled cyst’ as a cavitary lesion with a wall thickness of 4 mm or less along at least 75% of the circumference of the lesion. The whole group underwent post-operative follow-up. Results The incidence of cystic lung cancer was 0.49% (24/4,897 of surgical cases. The subjects’ age ranged from 19 to 77 yr with a median age of 56.5 yr. Ten cases presented with respiratory symptoms while 14 showed abnormal shadows on a chest CT without symptoms. Histological analysis showed that 18 cases were of adenocarcinoma, three of squamous cell carcinoma, one of small cell carcinoma, one of adenosquamous carcinoma and one of large cell carcinoma. Three patients were dead, and the remaining 21 patients are alive and disease free at the end of follow-up. Conclusion Cystic lung cancer should be kept in mind during the differential diagnosis of focal benign cyst. Cystic lung cancer could achieve a good outcome if early diagnose can be obtained.

  11. Sub-Thz Vibrational Spectroscopy for Analysis of Ovarian Cancer Cells (United States)

    Ferrance, Jerome P.; Sizov, Igor; Jazaeri, Amir; Moyer, Aaron; Gelmont, Boris; Globus, Tatiana


    Sub-THz vibrational spectroscopy utilizes wavelengths in the submillimeter-wave range ( 1.5-30 wn), beyond those traditionally used for chemical and biomolecular analysis. This low energy radiation excites low-frequency internal molecular motions (vibrations) involving hydrogen bonds and other weak connections within these molecules. The ability of sub-THz spectroscopy to identify and quantify biological molecules is based on detection of signature resonance absorbance at specific frequencies between 0.05 and 1 THz, for each molecule. The long wavelengths of this radiation, mean that it can even pass through entire cells, detecting the combinations of proteins and nucleic acids that exist within the cell. This research introduces a novel sub-THz resonance spectroscopy instrument with spectral resolution sufficient to identify individual resonance absorption peaks, for the analysis of ovarian cancer cells. In vitro cell cultures of SK-OV-3 and ES-2 cells, two human ovarian cancer subtypes, were characterized and compared with a normal non-transformed human fallopian tube epithelial cell line (FT131). A dramatic difference was observed between the THz absorption spectra of the cancer and normal cell sample materials with much higher absorption intensity and a very strong absorption peak at a frequency of 13 wn dominating the cancer sample spectra. Comparison of experimental spectra with molecular dynamic simulated spectroscopic signatures suggests that the high intensity spectral peak could originate from overexpressed mi-RNA molecules specific for ovarian cancer. Ovarian cancer cells are utilized as a proof of concept, but the sub-THz spectroscopy method is very general and could also be applied to other types of cancer.

  12. Coffee drinking and pancreatic cancer risk: A meta-analysis of cohort studies

    Institute of Scientific and Technical Information of China (English)

    Jie Dong; Jian Zou; Xiao-Feng Yu


    AIM: To quantitatively assess the relationship between coffee consumption and incidence of pancreatic cancer in a meta-analysis of cohort studies.METHODS: We searched MEDLINE, EMBASE, Science Citation Index Expanded and bibliographies of retrieved articles. Studies were included if they reported relative risks (RRs) and corresponding 95% CIs of pancreatic cancer with respect to frequency of coffee intake. We performed random-effects meta-analyses and meta-regressions of study-specific incremental estimates to determine the risk of pancreatic cancer associated with a 1 cup/d increment in coffee consumption.RESULTS: Fourteen studies met the inclusion criteria, which included 671 080 individuals (1496 cancer events) with an average follow-up of 14.9 years. Compared with individuals who did not drink or seldom drank coffee per day, the pooled RR of pancreatic cancer was 0.82 (95% CI: 0.69-0.95) for regular coffee drinkers, 0.86 (0.76-0.96) for low to moderate coffee drinkers, and 0.68 (0.51-0.84) for high drinkers. In subgroup analy-ses, we noted that, coffee drinking was associated with a reduced risk of pancreatic cancer in men, while this association was not seen in women. These associations were also similar in studies from North America, Europe, and the Asia-Pacific region.CONCLUSION: Findings from this meta-analysis sug-gest that there is an inverse relationship between coffee drinking and risk of pancreatic cancer.. 2011 Baishideng. All rights reserved.

  13. Model-based methods for linkage analysis. (United States)

    Rice, John P; Saccone, Nancy L; Corbett, Jonathan


    The logarithm of an odds ratio (LOD) score method originated in a seminal article by Newton Morton in 1955. The method is broadly concerned with issues of power and the posterior probability of linkage, ensuring that a reported linkage has a high probability of being a true linkage. In addition, the method is sequential so that pedigrees or LOD curves may be combined from published reports to pool data for analysis. This approach has been remarkably successful for 50 years in identifying disease genes for Mendelian disorders. After discussing these issues, we consider the situation for complex disorders where the maximum LOD score statistic shares some of the advantages of the traditional LOD score approach, but is limited by unknown power and the lack of sharing of the primary data needed to optimally combine analytic results. We may still learn from the LOD score method as we explore new methods in molecular biology and genetic analysis to utilize the complete human DNA sequence and the cataloging of all human genes.

  14. Spatial Analysis Methods of Road Traffic Collisions

    DEFF Research Database (Denmark)

    Loo, Becky P. Y.; Anderson, Tessa Kate

    Spatial Analysis Methods of Road Traffic Collisions centers on the geographical nature of road crashes, and uses spatial methods to provide a greater understanding of the patterns and processes that cause them. Written by internationally known experts in the field of transport geography, the book...... outlines the key issues in identifying hazardous road locations (HRLs), considers current approaches used for reducing and preventing road traffic collisions, and outlines a strategy for improved road safety. The book covers spatial accuracy, validation, and other statistical issues, as well as link......-attribute and event-based approaches, cluster identification, and risk exposure....


    Directory of Open Access Journals (Sweden)

    Józef DREWNIAK


    Full Text Available In the present paper, planetary automatic transmission is modeled by means of contour graphs. The goals of modeling could be versatile: ratio calculating via algorithmic equation generation, analysis of velocity and accelerations. The exemplary gears running are analyzed, several drives/gears are consecutively taken into account discussing functional schemes, assigned contour graphs and generated system of equations and their solutions. The advantages of the method are: algorithmic approach, general approach where particular drives are cases of the generally created model. Moreover, the method allows for further analyzes and synthesis tasks e.g. checking isomorphism of design solutions.

  16. Comparison of virtual cystoscopy and ultrasonography for bladder cancer detection: A meta-analysis

    Energy Technology Data Exchange (ETDEWEB)

    Qu Xinhua; Huang Xiaolu [Department of Nuclear Medicine, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200127 (China); Department of Ultrasonic, Ninth People' s Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200011 (China); Wu Lianming [Department of Radiology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200127 (China); Huang Gang [Department of Nuclear Medicine, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200127 (China); Ping Xiong, E-mail: [Department of Ultrasonic, Ninth People' s Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200011 (China); Yan Weili, E-mail: [Department of Nuclear Medicine, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200127 (China)


    Background and purpose: Bladder cancer is the most commonly diagnosed malignancy in patients presenting with haematuria. Early detection is crucial for improving patient prognosis. We therefore performed a meta-analysis to evaluate and compare the detection validity (sensitivity and specificity) of virtual cystoscopy (VC) and ultrasonography (US). Methods: We searched MEDLINE, EMBASE, PubMed and the Cochrane Library for studies evaluating diagnosis validity of VC and US between January 1966 and December 2009. Meta-analysis methods were used to pool sensitivity and specificity and to construct a summary receiver-operating characteristic (SROC) curve. Results: A total of 26 studies that included 3084 patients who fulfilled all of the inclusion criteria were considered for inclusion in the analysis. The pooled sensitivity for bladder cancer detection using CT virtual cystoscopy (CTVC), MR virtual cystoscopy (MRVC) and US was 0.939 (95% CI, 0.919-0.956), 0.908 (95% CI, 0.827-0.959) and 0.779 (95% CI, 0.744-0.812), respectively. The pooled specificity for bladder cancer detection using CTVC, MRVC and US was 0.981 (95% CI, 0.973-0.988), 0.948 (95% CI, 0.884-0.983) and 0.962 (95% CI, 0.953-0.969), respectively. The pooled diagnostic odd ratio (DOR) estimate for CTVC (604.22) were significantly higher than for MRVC (144.35, P < 0.001) and US (72.472, P < 0.001). Conclusion: Our results showed that both CTVC and MRVC are better imaging methods for diagnosing bladder cancer than US. CTVC has higher diagnostic value (sensitivity, specificity and DOR) for the detection of bladder cancer than either MRCT or US.

  17. Text analysis devices, articles of manufacture, and text analysis methods (United States)

    Turner, Alan E; Hetzler, Elizabeth G; Nakamura, Grant C


    Text analysis devices, articles of manufacture, and text analysis methods are described according to some aspects. In one aspect, a text analysis device includes processing circuitry configured to analyze initial text to generate a measurement basis usable in analysis of subsequent text, wherein the measurement basis comprises a plurality of measurement features from the initial text, a plurality of dimension anchors from the initial text and a plurality of associations of the measurement features with the dimension anchors, and wherein the processing circuitry is configured to access a viewpoint indicative of a perspective of interest of a user with respect to the analysis of the subsequent text, and wherein the processing circuitry is configured to use the viewpoint to generate the measurement basis.

  18. Numerical methods and analysis of multiscale problems

    CERN Document Server

    Madureira, Alexandre L


    This book is about numerical modeling of multiscale problems, and introduces several asymptotic analysis and numerical techniques which are necessary for a proper approximation of equations that depend on different physical scales. Aimed at advanced undergraduate and graduate students in mathematics, engineering and physics – or researchers seeking a no-nonsense approach –, it discusses examples in their simplest possible settings, removing mathematical hurdles that might hinder a clear understanding of the methods. The problems considered are given by singular perturbed reaction advection diffusion equations in one and two-dimensional domains, partial differential equations in domains with rough boundaries, and equations with oscillatory coefficients. This work shows how asymptotic analysis can be used to develop and analyze models and numerical methods that are robust and work well for a wide range of parameters.

  19. Cloud Based Development Issues: A Methodical Analysis

    Directory of Open Access Journals (Sweden)

    Sukhpal Singh


    Full Text Available Cloud based development is a challenging task for various software engineering projects, especifically for those which demand extraordinary quality, reusability and security along with general architecture. In this paper we present a report on a methodical analysis of cloud based development problems published in major computer science and software engineering journals and conferences organized by various researchers. Research papers were collected from different scholarly databases using search engines within a particular period of time. A total of 89 research papers were analyzed in this methodical study and we categorized into four classes according to the problems addressed by them. The majority of the research papers focused on quality (24 papers associated with cloud based development and 16 papers focused on analysis and design. By considering the areas focused by existing authors and their gaps, untouched areas of cloud based development can be discovered for future research works.

  20. Quantitative gold nanoparticle analysis methods: A review. (United States)

    Yu, Lei; Andriola, Angelo


    Research and development in the area of gold nanoparticles' (AuNPs) preparation, characterization, and applications are burgeoning in recent years. Many of the techniques and protocols are very mature, but two major concerns are with the mass domestic production and the consumption of AuNP based products. First, how many AuNPs exist in a dispersion? Second, where are the AuNPs after digestion by the environment and how many are there? To answer these two questions, reliable and reproducible methods are needed to analyze the existence and the population of AuNP in samples. This review summarized the most recent chemical and particle quantitative analysis methods that have been used to characterize the concentration (in number of moles of gold per liter) or population (in number of particles per mL) of AuNPs. The methods summarized in this review include, mass spectroscopy, electroanalytical methods, spectroscopic methods, and particle counting methods. These methods may count the number of AuNP directly or analyze the total concentration of element gold in an AuNP dispersion.

  1. Application of HPLC Combined with Laser Induced Fluorescence for Protein Profile Analysis of Tissue Homogenates in Cervical Cancer


    Sujatha Bhat; Ajeetkumar Patil; Lavanya Rai; Kartha, V. B.; Santhosh Chidangil


    A highly objective method, High Performance Liquid Chromatography with Laser Induced Fluorescence (HPLC-LIF) technique was used to study the protein profiles of normal and cervical cancer tissue homogenates. A total of 44 samples including normal cervical biopsy samples from the hysterectomy patients and the patients suffering from different stages of the cervical cancer were recorded by HPLC-LIF and analysed by Principle Component Analysis (PCA) to get statistical information on different t...

  2. Comparison of Robotic Surgery with Laparoscopy and Laparotomy for Treatment of Endometrial Cancer: A Meta-Analysis


    Longke Ran; Jing Jin; Yan Xu; Youquan Bu; Fangzhou Song


    Purpose To compare the relative merits among robotic surgery, laparoscopy, and laparotomy for patients with endometrial cancer by conducting a meta-analysis. Methods The MEDLINE, Embase, PubMed, Web of Science, and Cochrane Library databases were searched. Studies clearly documenting a comparison between robotic surgery and laparoscopy or between robotic surgery and laparotomy for endometrial cancer were selected. The outcome measures included operating time (OT), number of complications, len...

  3. Single-cell analysis - Methods and protocols

    Directory of Open Access Journals (Sweden)

    Carlo Alberto Redi


    Full Text Available This is certainly a timely volume in the Methods in molecular biology series: we already entered the synthetic biology era and thus we need to be aware of the new methodological advances able to fulfill the new and necessary needs for biologists, biotechnologists and nano-biotechnologists. Notably, among these, the possibility to perform single cell analysis allow researchers to capture single cell responses....

  4. Pattern of nodal involvement in papillary thyroid cancer: a challenge of quantitative analysis


    Fama, Fausto; Cicciù, Marco; Giudice, Giuseppe Lo; Sindoni, Alessandro; Palella, Jessica; Piquard, Arnaud; Saint-Marc, Olivier; Benvenga, Salvatore; Bramanti, Ennio; Cervino, Gabriele; Florio, Maria Gioffre


    Introduction: Backgrounds of this study were to examine and analyse the relationship among the number of lymph nodes with metastases harvested in central and lateral compartments, the characteristics of tumours and patients, and the recurrences rate. Methods: A retrospective review of 118 patients treated for a papillary thyroid cancer and underwent to neck dissection, including in all cases both central and lateral compartment, was realised. A quantitative analysis, on this homogeneous cohor...

  5. Cruciferous vegetable consumption and the risk of pancreatic cancer: a meta-analysis


    Li, Li-yi; Luo, Yue; Lu, Ming-Dong; Xu, Xiao-Wu; Lin, Hai-duo; Zheng, Zhi-Qiang


    Background Previous studies regarding the association between cruciferous vegetable intake and pancreatic cancer risk have reported inconsistent results. We conducted a meta-analysis to demonstrate the potential association between them. Methods A systematic literature search of papers was conducted in March 2014 using PubMed, EMBASE, and Web of Science, and the references of the retrieved articles were screened. The summary odds ratios (ORs) with 95% confidence interval (CI) for the highest ...

  6. Comparative analysis of clinicopathological correlations of cyclooxygenase-2 expression in resectable pancreatic cancer

    Institute of Scientific and Technical Information of China (English)

    Marketa; Hermanova; Petr; Karasek; Jiri; Tomasek; Jiri; Lenz; Jiri; Jarkovsky; Petr; Dite


    AIM:To perform a comparative analysis of clinicopathological correlations of cyclooxygenase2 (COX2) expression in pancreatic cancer, examined by monoclonal and polyclonal antibodies.METHODS: The COX2 expression in 85 resection specimens of pancreatic ductal adenocarcinoma was immunohistochemically examined using both monoclonal and polyclonal antibodies. The final immunoscores were obtained by multiplying the percentage of positive cells with the numeric score reflecting the staining intensity.COX2 expressi...

  7. A Western Dietary Pattern Increases Prostate Cancer Risk: A Systematic Review and Meta-Analysis


    Roberto Fabiani; Liliana Minelli; Gaia Bertarelli; Silvia Bacci


    Dietary patterns were recently applied to examine the relationship between eating habits and prostate cancer (PC) risk. While the associations between PC risk with the glycemic index and Mediterranean score have been reviewed, no meta-analysis is currently available on dietary patterns defined by “a posteriori” methods. A literature search was carried out (PubMed, Web of Science) to identify studies reporting the relationship between dietary patterns and PC risk. Relevant dietary patterns wer...

  8. Analysis of Fiber deposition using Automatic Image Processing Method (United States)

    Belka, M.; Lizal, F.; Jedelsky, J.; Jicha, M.


    Fibers are permanent threat for a human health. They have an ability to penetrate deeper in the human lung, deposit there and cause health hazards, e.glung cancer. An experiment was carried out to gain more data about deposition of fibers. Monodisperse glass fibers were delivered into a realistic model of human airways with an inspiratory flow rate of 30 l/min. Replica included human airways from oral cavity up to seventh generation of branching. Deposited fibers were rinsed from the model and placed on nitrocellulose filters after the delivery. A new novel method was established for deposition data acquisition. The method is based on a principle of image analysis. The images were captured by high definition camera attached to a phase contrast microscope. Results of new method were compared with standard PCM method, which follows methodology NIOSH 7400, and a good match was found. The new method was found applicable for evaluation of fibers and deposition fraction and deposition efficiency were calculated afterwards.

  9. Analysis of Fiber deposition using Automatic Image Processing Method

    Directory of Open Access Journals (Sweden)

    Jicha M.


    Full Text Available Fibers are permanent threat for a human health. They have an ability to penetrate deeper in the human lung, deposit there and cause health hazards, e.glung cancer. An experiment was carried out to gain more data about deposition of fibers. Monodisperse glass fibers were delivered into a realistic model of human airways with an inspiratory flow rate of 30 l/min. Replica included human airways from oral cavity up to seventh generation of branching. Deposited fibers were rinsed from the model and placed on nitrocellulose filters after the delivery. A new novel method was established for deposition data acquisition. The method is based on a principle of image analysis. The images were captured by high definition camera attached to a phase contrast microscope. Results of new method were compared with standard PCM method, which follows methodology NIOSH 7400, and a good match was found. The new method was found applicable for evaluation of fibers and deposition fraction and deposition efficiency were calculated afterwards.

  10. Excision repair cross complementation group 1 polymorphisms and lung cancer risk: a meta-analysis

    Institute of Scientific and Technical Information of China (English)

    CAO Chao; DENG Zai-chun; ZHANG Yan-mei; WANG Ran; SUN Shi-fang; CHEN Zhong-bo; MA Hong-ying; YU Yi-ming; DING Qun-li; SHU Li-hua


    Background Several studies have evaluated the association between polymorphisms of encoding excision repair cross complementation group 1 (ERCC1) enzyme and lung cancer risk in diverse populations but with conflicting results.By pooling the relatively small samples in each study, it is possible to perform a meta-analysis of the evidence by rigorous methods.Methods Embase, Ovid, Medline and Chinese National Knowledge Infrastructure were searched. Additional studies were identified from references in original studies or review articles. Articles meeting the inclusion criteria were reviewed systematically, and the reported data were aggregated using the statistical techniques of meta-analysis.Results We found 3810 cases with lung cancer and 4332 controls from seven eligible studies. T19007C polymorphism showed no significant effect on lung cancer risk (C allele vs. T allele: odds ratio (OR)=0.91, 95% confidence interval (CI)=0.80-1.04; CC vs. TT: OR=0.76, 95% CI=0.56-1.02; CC vs. (CT+TT): OR=0.96, 95% CI=-0.84-1.10). Similarly,there was no significant main effects for T19007C polymorphism on lung cancer risk when stratified analyses by ethnicity (Chinese or Caucasian). No significant association was found between C8092A polymorphism (3060 patients and 2729 controls) and the risk of lung cancer (A allele vs. C allele: OR=1.03, 95% CI=0.95-1.11; AA vs. CC: OR=1.08, 95% CI=-0.88-1.33; AA vs. (AC+CC): OR=1.08, 95% CI=-0.88-1.31).Conclusion We found little evidence of an association between the T1900C or C8092A polymorphisms of ERCC 1 and the risk of lung cancer in Caucasian or Han Chinese people.

  11. Clinical Omics Analysis of Colorectal Cancer Incorporating Copy Number Aberrations and Gene Expression Data

    Directory of Open Access Journals (Sweden)

    Tsuyoshi Yoshida


    Full Text Available Background: Colorectal cancer (CRC is one of the most frequently occurring cancers in Japan, and thus a wide range of methods have been deployed to study the molecular mechanisms of CRC. In this study, we performed a comprehensive analysis of CRC, incorporating copy number aberration (CRC and gene expression data. For the last four years, we have been collecting data from CRC cases and organizing the information as an “omics” study by integrating many kinds of analysis into a single comprehensive investigation. In our previous studies, we had experienced difficulty in finding genes related to CRC, as we observed higher noise levels in the expression data than in the data for other cancers. Because chromosomal aberrations are often observed in CRC, here, we have performed a combination of CNA analysis and expression analysis in order to identify some new genes responsible for CRC. This study was performed as part of the Clinical Omics Database Project at Tokyo Medical and Dental University. The purpose of this study was to investigate the mechanism of genetic instability in CRC by this combination of expression analysis and CNA, and to establish a new method for the diagnosis and treatment of CRC. Materials and methods: Comprehensive gene expression analysis was performed on 79 CRC cases using an Affymetrix Gene Chip, and comprehensive CNA analysis was performed using an Affymetrix DNA Sty array. To avoid the contamination of cancer tissue with normal cells, laser micro-dissection was performed before DNA/RNA extraction. Data analysis was performed using original software written in the R language. Result: We observed a high percentage of CNA in colorectal cancer, including copy number gains at 7, 8q, 13 and 20q, and copy number losses at 8p, 17p and 18. Gene expression analysis provided many candidates for CRC-related genes, but their association with CRC did not reach the level of statistical significance. The combination of CNA and gene

  12. Microarray-based analysis of microRNA expression in breast cancer stem cells

    Directory of Open Access Journals (Sweden)

    Wang Zhi-xin


    Full Text Available Abstract Background This study aimed to determine the miRNA profile in breast cancer stem cells (BCSCs and to explore the functions of characteristic BCSC miRNAs. Methods We isolated ESA+CD44+CD24-/low BCSCs from MCF-7 cells using fluorescence-activated cell sorting (FACS. A human breast cancer xenograft assay was performed to validate the stem cell properties of the isolated cells, and microarray analysis was performed to screen for BCSC-related miRNAs. These BCSC-related miRNAs were selected for bioinformatic analysis and target prediction using online software programs. Results The ESA+CD44+CD24-/low cells had up to 100- to 1000-fold greater tumor-initiating capability than the MCF-7 cells. Tumors initiated from the ESA+CD44+CD24-/low cells were included of luminal epithelial and myoepithelial cells, indicating stem cell properties. We also obtained miRNA profiles of ESA+CD44+CD24-/low BCSCs. Most of the possible targets of potential tumorigenesis-related miRNAs were oncogenes, anti-oncogenes or regulatory genes. Conclusions We identified a subset of miRNAs that were differentially expressed in BCSCs, providing a starting point to explore the functions of these miRNAs. Evaluating characteristic BCSC miRNAs represents a new method for studying breast cancer-initiating cells and developing therapeutic strategies aimed at eradicating the tumorigenic subpopulation of cells in breast cancer.

  13. Selectively starving cancer cells through dietary manipulation: methods and clinical implications. (United States)

    Simone, Brittany A; Champ, Colin E; Rosenberg, Anne L; Berger, Adam C; Monti, Daniel A; Dicker, Adam P; Simone, Nicole L


    As the link between obesity and metabolic syndrome and cancer becomes clearer, the need to determine the optimal way to incorporate dietary manipulation in the treatment of cancer patients becomes increasingly important. Metabolic-based therapies, such as caloric restriction, intermittent fasting and a ketogenic diet, have the ability to decrease the incidence of spontaneous tumors and slow the growth of primary tumors, and may have an effect on distant metastases in animal models. Despite the abundance of preclinical data demonstrating the benefit of dietary modification for cancer, to date there are few clinical trials targeting diet as an intervention for cancer patients. We hypothesize that this may be due, in part, to the fact that several different types of diet modification exist with no clear recommendations regarding the optimal method. This article will delineate three commonly used methods of dietary manipulation to assess the potential of each as a regimen for cancer therapy.

  14. Menstrual Factors,Reproductive Factors and Lung Cancer Risk:A Meta-analysis

    Institute of Scientific and Technical Information of China (English)

    Yue ZHANG; Zhihua YIN; Li SHEN; Yan WAN; Baosen ZHOU


    Background and objective Epidemiological studies have suggested that menstrual and reproductive factors may influence lung cancer risk,but the results are controversial.We therefore carried out a meta-analysis aiming to examine the associations of lung cancer in women with menstrual and reproductive factors.Methods Relevant studies were searched from PubMed database,CNKI,WANFANG DATA and VIP INFORMATION up to January 2012,with no language restrictions.References listed from selected papers were also reviewed.We included studies that reported the estimates of relative risks(RRs)with 95% confidence intervals(CIs)for the association between menstrual and reproductive factors and lung cancer risk.The pooled RRs were calculated after the heterogeneity test with the software Stata 11,and publication bias and sensitivity were evaluated at the same time.Results Twenty-five articles,representing 24 independent studies,were included in this meta-analysis.Older age at menarche in North America women(RR=0.83;95%CI:0.73-0.94)was associated with a significant decreased risk of lung cancer.Longer length of menstrual cycle was also associated with decreased lung cancer risk(RR=0.72;95%CI:0.57-0.90).Other exposures were not significantly associated.Conclusions Our analysis provides evidence of the hypothesis that female sex hormones influence the risk of lung cancer in women,yet additional studies are warranted to extend this finding and to clarify the underlying mechanisms.

  15. Wood dust exposure and lung cancer risk: a meta-analysis. (United States)

    Hancock, David G; Langley, Mary E; Chia, Kwan Leung; Woodman, Richard J; Shanahan, E Michael


    Occupational lung cancers represent a major health burden due to their increasing prevalence and poor long-term outcomes. While wood dust is a confirmed human carcinogen, its association with lung cancer remains unclear due to inconsistent findings in the literature. We aimed to clarify this association using meta-analysis. We performed a search of 10 databases to identify studies published until June 2014. We assessed the lung cancer risk associated with wood dust exposure as the primary outcome and with wood dust-related occupations as a secondary outcome. Random-effects models were used to pool summary risk estimates. 85 publications were included in the meta-analysis. A significantly increased risk for developing lung cancer was observed among studies that directly assessed wood dust exposure (RR 1.21, 95% CI 1.05 to 1.39, n=33) and that assessed wood dust-related occupations (RR 1.15, 95% CI 1.07 to 1.23, n=59). In contrast, a reduced risk for lung cancer was observed among wood dust (RR 0.63, 95% CI 0.39 to 0.99, n=5) and occupation (RR 0.96, 95% CI 0.95 to 0.98, n=1) studies originating in Nordic countries, where softwood dust is the primary exposure. These results were independent of the presence of adjustment for smoking and exposure classification methods. Only minor differences in risk between the histological subtypes were identified. This meta-analysis provides strong evidence for an association between wood dust and lung cancer, which is critically influenced by the geographic region of the study. The reasons for this region-specific effect estimates remain to be clarified, but may suggest a differential effect for hardwood and softwood dusts.

  16. Pathway analysis for genome-wide association study of lung cancer in Han Chinese population.

    Directory of Open Access Journals (Sweden)

    Ruyang Zhang

    Full Text Available Genome-wide association studies (GWAS have identified a number of genetic variants associated with lung cancer risk. However, these loci explain only a small fraction of lung cancer hereditability and other variants with weak effect may be lost in the GWAS approach due to the stringent significance level after multiple comparison correction. In this study, in order to identify important pathways involving the lung carcinogenesis, we performed a two-stage pathway analysis in GWAS of lung cancer in Han Chinese using gene set enrichment analysis (GSEA method. Predefined pathways by BioCarta and KEGG databases were systematically evaluated on Nanjing study (Discovery stage: 1,473 cases and 1,962 controls and the suggestive pathways were further to be validated in Beijing study (Replication stage: 858 cases and 1,115 controls. We found that four pathways (achPathway, metPathway, At1rPathway and rac1Pathway were consistently significant in both studies and the P values for combined dataset were 0.012, 0.010, 0.022 and 0.005 respectively. These results were stable after sensitivity analysis based on gene definition and gene overlaps between pathways. These findings may provide new insights into the etiology of lung cancer.

  17. P53 codon 72 polymorphism and ovarian cancer risk: a meta-analysis

    Institute of Scientific and Technical Information of China (English)

    Zhizhong Zhang; Cuangbo Fu; Meilin Wang; Na Tong; Shizhi Wang; Zhengdong Zhang


    Objective: p53 is a tumor suppressor gene and is involved in the etiology of ovarian cancer. Studies investigating the associations between the p53 codon 72 polymorphism and ovarian cancer risk showed conflicting results. We performed this meta-analysis from eligible studies to evaluate this purported relationship. Methods: This meta-analysis was performed from 9 case-control studies, including 825 ovarian cases and 1073 controls. The fixed and random effect models were used to estimate the odds ratios(ORs) for various contrasts of this polymorphism. Results: The combined results based on all studies showed that a significantly decreased risk was associated with the variant Pro/Pro genotype, compared with Arg/Pro+Arg/Arg genotypes(OR, 0.70; 95%CI, 0.51-0.95). When stratifying the studies by ethnicity, we found that individuals with the variant genotype Pro/Pro had a significantly decreased risk of ovarian cancer compared with Arg/Arg genotype(OR, 0.43; 95%CI, 0.20-0.89) and Arg/Pro+Arg/Arg genotypes(OR, 0.61; 95%CI, 0.37-0.99) among Africans. Conclusion: This meta-analysis suggests that the p53 codon 72 polymorphism may contribute to genetic susceptibility to ovarian cancer. More studies based on larger sample size should be performed to confirm the findings.

  18. Usefulness of liquid-based cytology in hormone receptor analysis of breast cancer specimens. (United States)

    Nishimura, Rieko; Aogi, Kenjiro; Yamamoto, Tamami; Takabatake, Daisuke; Takashima, Seiki; Teramoto, Norihiro; Kagawa, Akihiro; Morita, Sachiko


    Immunohistochemical (IHC) analysis of the hormone receptor (HR) in breast cancer cytology is an important issue nowadays. Several studies have shown discrepancy in the HR status between the primary tumor and metastases. Cytology can be used for patients with metastatic disease. Although cytological assessment of HR is an excellent method, it has not been routinely used because of the difficulty in consistently preparing multiple good quality slides. Liquid-based cytology (LBC) preparation is considered as the key to resolving the aforementioned problem; however, few studies have reported the HR assessment in breast cancer using LBC. Therefore, the HR status of LBC slides from 82 breast cancers was compared with that of the corresponding surgical specimens. The HR assay in both the LBC slides and surgical specimens was conducted by IHC using an autostainer. For the IHC staining, the protocol recommended by the manufacturer for paraffin-embedded sections was used for both the cytology and histology specimens. The HR results of the cytology agreed with those of the histology in 80 of the 82 cases (accuracy rate, 98%) for estrogen receptor, and in 78 of the 82 cases (accuracy rate, 95%) for progesterone receptor. The overall accuracy of the HR status on the cytology and the histology was 99% in 81 of the 82 cases. In conclusion, in HR analysis of breast cancers, LBC followed by IHC using an autostainer was useful for the standard processing of cytological specimens and showed a good correlation with the results of analysis on the histology specimens.

  19. Statins and the risk of lung cancer: a meta-analysis.

    Directory of Open Access Journals (Sweden)

    Min Tan

    Full Text Available PURPOSE: Several epidemiologic studies have evaluated the association between statins and lung cancer risk, whereas randomized controlled trials (RCTs on cardiovascular outcomes provide relevant data as a secondary end point. We conducted a meta-analysis of all relevant studies to examine this association. METHODS: A systematic literature search up to March 2012 was performed in PubMed database. Study-specific risk estimates were pooled using a random-effects model. RESULTS: Nineteen studies (5 RCTs and 14 observational studies involving 38,013 lung cancer cases contributed to the analysis. They were grouped on the basis of study design, and separate meta-analyses were conducted. There was no evidence of an association between statin use and risk of lung cancer either among RCTs (relative risk [RR] 0.91, 95% confidence interval [CI] 0.76-1.09, among cohort studies (RR 0.94, 95% CI 0.82-1.07, or among case-control studies (RR 0.82, 95% CI 0.57-1.16. Low evidence of publication bias was found. However, statistically significant heterogeneity was found among cohort studies and among case-control studies. After excluding the studies contributing most to the heterogeneity, summary estimates were essentially unchanged. CONCLUSION: The results of our meta-analysis suggest that there is no association between statin use and the risk of lung cancer.

  20. Space Debris Reentry Analysis Methods and Tools

    Institute of Scientific and Technical Information of China (English)

    WU Ziniu; HU Ruifeng; QU Xi; WANG Xiang; WU Zhe


    The reentry of uncontrolled spacecraft may be broken into many pieces of debris at an altitude in the range of 75-85 km.The surviving fragments could pose great hazard and risk to ground and people.In recent years,methods and tools for predicting and analyzing debris reentry and ground risk assessment have been studied and developed in National Aeronautics and Space Administration(NASA),European Space Agency(ESA) and other organizations,including the group of the present authors.This paper reviews the current progress on this topic of debris reentry briefly.We outline the Monte Carlo method for uncertainty analysis,breakup prediction,and parameters affecting survivability of debris.The existing analysis tools can be classified into two categories,i.e.the object-oriented and the spacecraft-oriented methods,the latter being more accurate than the first one.The past object-oriented tools include objects of only simple shapes.For more realistic simulation,here we present an object-oriented tool debris reentry and ablation prediction system(DRAPS) developed by the present authors,which introduces new object shapes to 15 types,as well as 51 predefined motions and relevant aerodynamic and aerothermal models.The aerodynamic and aerothermal models in DRAPS are validated using direct simulation Monte Carlo(DSMC) method.

  1. Feasibility of MR metabolomics for immediate analysis of resection margins during breast cancer surgery.

    Directory of Open Access Journals (Sweden)

    Tone F Bathen

    Full Text Available In this study, the feasibility of high resolution magic angle spinning (HR MAS magnetic resonance spectroscopy (MRS of small tissue biopsies to distinguish between tumor and non-involved adjacent tissue was investigated. With the current methods, delineation of the tumor borders during breast cancer surgery is a challenging task for the surgeon, and a significant number of re-surgeries occur. We analyzed 328 tissue samples from 228 breast cancer patients using HR MAS MRS. Partial least squares discriminant analysis (PLS-DA was applied to discriminate between tumor and non-involved adjacent tissue. Using proper double cross validation, high sensitivity and specificity of 91% and 93%, respectively was achieved. Analysis of the loading profiles from both principal component analysis (PCA and PLS-DA showed the choline-containing metabolites as main biomarkers for tumor content, with phosphocholine being especially high in tumor tissue. Other indicative metabolites include glycine, taurine and glucose. We conclude that metabolic profiling by HR MAS MRS may be a potential method for on-line analysis of resection margins during breast cancer surgery to reduce the number of re-surgeries and risk of local recurrence.

  2. Stability analysis of liver cancer-related microRNAs

    Institute of Scientific and Technical Information of China (English)

    Yan Li; Zhenggang Jiang; Lijian Xu; Hu Yao; Jiangfeng Guo; Xianfeng Ding


    MicroRNAs(miRNAs)are non-coding,single-stranded RNAs of ~22 nt and constitute a novel class of gene regulators that are found in both plants and animals.Several studies have demonstrated that serum miRNAs could serve as potential biomarkers for the detection of various cancers and other diseases.A few documents regarding the stability of liver cancer-related miRNAs in serum are available.A systemic analysis of the stability of miRNA in serum is quite necessary.The purpose of this study was to evaluate the stability of miRNAs from three different sources,cultured liver cancer Huh-7 cell line,clinical liver cancer,and serum under different experimental conditions,including different temperature,time duration,pH values,Rnase A digestion,Dnase Ⅰ digestion,and various freeze-thaw cycles.The qRT-PCR analysis demonstrated that liver cancer-related miRNAs were detectable under each of test conditions,indicating that miRNAs were extremely stable and resistant to destruction and degradation under harsh environmental conditions.However,ribosomal RNA was fragile and easily degraded by demonstrating sharp decrease of relative expression under the non-physiological test conditions.We also established a robust procedure for serum RNA extraction,which is greatly important not only for the miRNA profiling studies bat also for the disease prognosis based on abnormal miRNA expression.

  3. Better exercise adherence after treatment for cancer (BEAT Cancer) study: Rationale, design, and methods


    Rogers, Laura Q; McAuley, Edward; Anton, Philip M.; Courneya, Kerry S.; Vicari, Sandra; Hopkins-Price, Patricia; Verhulst, Steven; Mocharnuk, Robert; Hoelzer, Karen


    Most breast cancer survivors do not engage in regular physical activity. Our physical activity behavior change intervention for breast cancer survivors significantly improved physical activity and health outcomes post-intervention during a pilot, feasibility study. Testing in additional sites with a larger sample and longer follow-up is warranted to confirm program effectiveness short and longer term. Importantly, the pilot intervention resulted in changes in physical activity and social cogn...

  4. Analysis and estimation of risk management methods

    Directory of Open Access Journals (Sweden)

    Kankhva Vadim Sergeevich


    Full Text Available At the present time risk management is an integral part of state policy in all the countries with developed market economy. Companies dealing with consulting services and implementation of the risk management systems carve out a niche. Unfortunately, conscious preventive risk management in Russia is still far from the level of standardized process of a construction company activity, which often leads to scandals and disapproval in case of unprofessional implementation of projects. The authors present the results of the investigation of the modern understanding of the existing methodology classification and offer the authorial concept of classification matrix of risk management methods. Creation of the developed matrix is based on the analysis of the method in the context of incoming and outgoing transformed information, which may include different elements of risk control stages. So the offered approach allows analyzing the possibilities of each method.

  5. Data Analysis Methods for Library Marketing (United States)

    Minami, Toshiro; Kim, Eunja

    Our society is rapidly changing to information society, where the needs and requests of the people on information access are different widely from person to person. Library's mission is to provide its users, or patrons, with the most appropriate information. Libraries have to know the profiles of their patrons, in order to achieve such a role. The aim of library marketing is to develop methods based on the library data, such as circulation records, book catalogs, book-usage data, and others. In this paper we discuss the methodology and imporatnce of library marketing at the beginning. Then we demonstrate its usefulness through some examples of analysis methods applied to the circulation records in Kyushu University and Guacheon Library, and some implication that obtained as the results of these methods. Our research is a big beginning towards the future when library marketing is an unavoidable tool.

  6. Optical methods for the analysis of dermatopharmacokinetics (United States)

    Lademann, Juergen; Weigmann, Hans-Juergen; von Pelchrzim, R.; Sterry, Wolfram


    The method of tape stripping in combination with spectroscopic measurements is a simple and noninvasive method for the analysis of dermatopharmacokinetics of cosmetic products and topically applied drugs. The absorbance at 430 nm was used for the characterization of the amount of corneocytes on the tape strips. It was compared to the increase of weight of the tapes after removing them from the skin surface. The penetration profiles of two UV filter substances used in sunscreens were determined. The combined method of tape stripping and spectroscopic measurements can be also used for the investigation of the dermatopharmacokinetics of topically applied drugs passing through the skin. Differences in the penetration profiles of the steroid compound clobetasol, applied in the same concentration in different formulations on the skin are presented.

  7. Metabolism and cell shape in cancer: a fractal analysis. (United States)

    D'Anselmi, Fabrizio; Valerio, Mariacristina; Cucina, Alessandra; Galli, Luca; Proietti, Sara; Dinicola, Simona; Pasqualato, Alessia; Manetti, Cesare; Ricci, Giulia; Giuliani, Alessandro; Bizzarri, Mariano


    Fractal analysis in cancer cell investigation provided meaningful insights into the relationship between morphology and phenotype. Some reports demonstrated that changes in cell shape precede and trigger dramatic modifications in both gene expression and enzymatic function. Nonetheless, metabolomic pattern in cells undergoing shape changes have been not still reported. Our study was aimed to investigate if modifications in cancer cell morphology are associated to relevant transition in tumour metabolome, analyzed by nuclear magnetic resonance spectroscopy and principal component analysis. MCF-7 and MDA-MB-231 breast cancer cells, exposed to an experimental morphogenetic field, undergo a dramatic change in their membrane profiles. Both cell lines recover a more rounded shape, loosing spindle and invasive protrusions, acquiring a quite "normal" morphology. This result, quantified by fractal analysis, shows that normalized bending energy (a global shape characterization expressing the amount of energy needed to transform a specific shape into its lowest energy state) decreases after 48 h. Later on, a significant shift from a high to a low glycolytic phenotype was observed on both cell lines: glucose flux begins to drop off at 48 h, leading to reduced lactate accumulation, and fatty acids and citrate synthesis slow-down after 72 h. Moreover, de novo lipidogenesis is inhibited and nucleotide synthesis is reduced, as indicated by the positive correlation between glucose and formate. In conclusion, these data indicate that the reorganization of cell membrane architecture, induced by environmental cues, is followed by a relevant transition of the tumour metabolome, suggesting cells undergo a dramatic phenotypic reversion.

  8. Clinical Analysis of Lung Cancer Patients Younger Than 30 Years

    Directory of Open Access Journals (Sweden)

    Guangjie HOU


    Full Text Available Background and objective It is common recognized that young patients of lung cancer have poor prognosis due to relatively higher malignancy and more invasive growth. In the past most studies on young patients of lung cancer selected patients younger than 40 or 45 years old, and there were few clinical materials for younger patients under 30 years. This study retrospectively described the the disease history, stage, treatment and pathology features of lung cancer patients younger than 30 years and aimed to provide references for these patients. Methods Those patients younger than 30 years, once admitted in the General Hospital of the People's Liberation Army for lung cancer from 1993 to date, were sought in medical record system, and 53 patients were found in total. In this group, there were 34 non-small cell lung cancer (NSCLC patients and 19 small cell lung cacer (SCLC patients. The male/female ratio was 1.5:1. In the NSCLC patients, there were 27 adenocarcinomas, 6 squamous carcinomas and 1 adenosquamous carcinoma, with no large cell carcinoma involved. In these patients, 12 patients received operations while 38 patients got chemo- and/or radiotherapy and 3 quited any treatment. Results There was no death in hospital, however, in the 12 patients who got operation, only 8 patients got complete resection while 4 patients got palliative resection. Conclusion Lung cancer patients younger than 30 years had a high fraction of adenocarcinoma and small cell type pathologically and most of them were in late stage when presenting with symptoms in hospital and would have a dismal prognosis. The routine health examination and early diagnosis should be emphasized to improve the prognosis of these patients.

  9. Investigation and analysis of oncologists' knowledge of morphine usage in cancer pain treatment

    Directory of Open Access Journals (Sweden)

    Liu W


    Full Text Available Weiran Liu,1,* Shumin Xie,2,* Lin Yue,3,* Jiahao Liu,2 Stephanie Mu-Lian Woo,4 Weilin Liu,2 Adam R Miller,5 Jing Zhang,6 Lijun Huang,7 Lei Zhang8,*1Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Department of Anesthesia, Tianjin, People's Republic of China; 2The Xiangya Medical School of Central-South University, Changsha, People's Republic of China; 3Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Outpatient Service, Tianjin, People's Republic of China; 4Harvard University, Cambridge, MA, USA; 5Indiana University School of Medicine, Indianapolis, IN, USA; 6Tianjin Medical University, Tianjin, People's Republic of China; 7Hunan Provincial Tumor Hospital, Department of Lymphoma and Hematology, Changsha, People's Republic of China; 8Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Lung Cancer Center, Department of Thoracic Surgery, Tianjin, People's Republic of China *These authors contributed equally to this paperPurpose: To examine oncologists' knowledge of cancer pain and morphine's clinical application in the People's Republic of China. In addition, this study analyzes and discusses the negative factors that currently affect the clinical application of morphine.Patients and methods: A questionnaire survey was given to a random sample of 150 oncologists from Tianjin Medical University Cancer Institute and Hospital. The statistical results were analyzed and processed using SPSS version 21.0 and Matlab version 2012a statistical software. Single-factor analysis of variance, Kruskal–Wallis nonparametric test, and independent samples t-test were adopted to analyze the difference in knowledge scores of morphine usage. The study

  10. What are the most effective methods for assessment of nutritional status in outpatients with gastric and colorectal cancer?

    Directory of Open Access Journals (Sweden)

    Mariana Abe Vicente


    Full Text Available Objective: To evaluate methods for the identification of nutrition risk and nutritional status in outpatients with colorectal (CRC and gastric cancer (GC, and to compare the results to those obtained for patients already treated for these cancers. Methods: A cross-sectional study was conducted on 137 patients: group 1 (n = 75 consisting of patients with GC or CRC, and group 2 (n = 62 consisting of patients after treatment of GC or CRC under follow up, who were tumor free for a period longer than 3 months. Nutritional status was assessed in these patients using objective methods ; nutritional screening tools [Malnutrition Universal Screening Tool (MUST, Malnutrition Screening Tool (MST, Nutritional Risk Index (NRI], and subjective assessment [Patient-Generated Subjective Global Assessment (PG-SGA]. The sensitivity and specificity of each method was calculated in relation to the PG-SGA used as gold standard. Results: One hundred thirty seven patients participated in the study. Stage IV cancer patients were more common in group 1. There was no difference in BMI between groups (p = 0.67. Analysis of the association between methods of assessing nutritional status and PG-SGA showed that the nutritional screening tools provided more significant results (p < 0.05 than the objective methods in the two groups. PG-SGA detected the highest proportion of undernourished patients in group 1. The nutritional screening tools MUST, NRI and MST were more sensitive than the objective methods. Phase angle measurement was the most sensitive objective method in group 1. Conclusion: The nutritional screening tools showed the best association with PG-SGA and were also more sensitive than the objective methods. The results suggest the combination of MUST and PG-SGA for patients with cancer before and after treatment.

  11. Relationship of Extreme Chromosomal Instability with Long-term Survival in a Retrospective Analysis of Primary Breast Cancer

    DEFF Research Database (Denmark)

    Roylance, Rebecca; Endesfelder, David; Gorman, Patricia


    methods, such as centromeric FISH, aimed at determining the variation around the modal number of two or more chromosomes within individual tumor nuclei. Here, we document the frequency of tumor CIN by dual centromeric FISH analysis in a retrospective primary breast cancer cohort of 246 patients...... with survival outcome. Results: There was increased CIN and clonal eterogeneity in ER-negative compared with ER-positive breast cancer. Consistent with a negative impact of CIN on cellular fitness, extreme CIN in ER-negative breast cancer was an independent variable associated with improved long-term survival......Background: Chromosomal instability (CIN) is thought to be associated with poor prognosis in solid tumors; however, evidence from preclinical and mouse tumor models suggest that CIN may paradoxically enhance or impair cancer cell fitness. Breast cancer prognostic expression signature sets, which...

  12. Contrast enhanced MR imaging of female pelvic cancers: Established methods and emerging applications

    Energy Technology Data Exchange (ETDEWEB)

    Punwani, Shonit, E-mail: [Department of Academic Radiology, 2nd Floor Podium, University College London Hospital, 235 Euston Road, London NW1 2BU (United Kingdom)


    Contrast enhanced magnetic resonance imaging of female pelvic cancers has been established for over 20 years. Conventional contrast enhanced imaging involves acquiring a set of pre-contrast T1 weighted images, followed by intravenous injection of an gadolinium based contrast agent and subsequent acquisition of a second set of contrast enhanced images. Developments in MR hardware and pulse sequences over the last 10 years have made dynamic contrast enhanced (DCE) protocols possible. DCE-MRI entails imaging of the same volume repeatedly prior to, during and following contrast injection. There have also been developments in image analysis methods and tools to reflect the increased data acquired. Qualitative analysis of contrast enhanced imaging (whether a single set or temporal series) by radiologists remains the mainstay for clinical reporting. Semi-quantitative assessment of signal intensity versus time curves and full pharmacokinetic modelling methods have emerged for evaluation of DCE-MRI data. DCE-MRI has found an established role in the detection, localisation and staging of female pelvic malignancies. Emerging applications of DCE-MRI include assessment of tumour grade, histology prior to and following treatment and prediction of individual and final treatment outcome. This article reviews the biophysical basis of contrast enhancement, the technical aspects of performance and analysis of DCE-MRI studies, and the established and emerging clinical utility of DCE-MRI in female pelvic malignancies.

  13. Estimating completeness of cancer registration in Saarland/Germany with capture-recapture methods. (United States)

    Brenner, H; Stegmaier, C; Ziegler, H


    Completeness of population-based cancer registration has been most commonly quantified by indirect measures, such as the death certificate only index or the mortality/incidence ratio. A major disadvantage of these measures is their strong dependence on the case fatality rate. Capture-recapture methodology offers an approach to estimate completeness directly which does not share this limitation. In this paper, a three-sources modelling approach is employed to derive estimates of completeness for the population-based cancer registry of Saarland. Overall, completeness is found to be high: estimates for all types of cancer range from 95.5 to 96.9% for calendar years 1970, 1975, 1980 and 1985. There is some variation with age (consistently high levels above age 30 years, a minimum of 87.7% in age group 15-29 years) and between cancer sites. Among the most common cancer sites, estimates of completeness are highest for gastrointestinal cancers (97.2%) and breast cancer (97.1%), while lower estimates of completeness are derived for cancers of the female genital organs (92.5%), the urinary tract (91.8%) and the prostate (91.0%). Although capture-recapture estimates are sensitive to the underlying assumptions about dependence between sources, careful application is encouraged to supplement traditional methods for evaluating completeness of cancer registration.

  14. Colorectal cancer mortality trends inSerbia during1991-2010:an age-period-cohort analysis anda joinpoint regression analysis

    Institute of Scientific and Technical Information of China (English)

    MilenaIlic; IrenaIlic


    Background:For both men and women worldwide, colorectal cancer is among the leading causes of cancer-related death. This study aimed to assess the mortality trends of colorectal cancer in Serbia between 1991 and 2010, prior to the introduction of population-based screening. Methods:Joinpoint regression analysis was used to estimate average annual percent change (AAPC) with the cor-responding 95% conifdence interval (CI). Furthermore, age-period-cohort analysis was performed to examine the effects of birth cohort and calendar period on the observed temporal trends. Results:We observed a signiifcantly increased trend in colorectal cancer mortality in Serbia during the study period (AAPC=1.6%, 95% CI 1.3%–1.8%). Colorectal cancer showed an increased mortality trend in both men (AAPC=2.0%, 95% CI 1.7%–2.2%) and women (AAPC=1.0%, 95% CI 0.6%–1.4%). The temporal trend of colorectal cancer mortality was signiifcantly affected by birth cohort (P Conclusions:We found that colorectal cancer mortality in Serbia increased considerably over the past two decades. Mortality increased particularly in men, but the trends were different according to age group and subsite. In Serbia, interventions to reduce colorectal cancer burden, especially the implementation of a national screening program, as well as treatment improvements and measures to encourage the adoption of a healthy lifestyle, are needed.

  15. Comparison of methods for estimating the intraclass correlation coefficient for binary responses in cancer prevention cluster randomized trials. (United States)

    Wu, Sheng; Crespi, Catherine M; Wong, Weng Kee


    The intraclass correlation coefficient (ICC) is a fundamental parameter of interest in cluster randomized trials as it can greatly affect statistical power. We compare common methods of estimating the ICC in cluster randomized trials with binary outcomes, with a specific focus on their application to community-based cancer prevention trials with primary outcome of self-reported cancer screening. Using three real data sets from cancer screening intervention trials with different numbers and types of clusters and cluster sizes, we obtained point estimates and 95% confidence intervals for the ICC using five methods: the analysis of variance estimator, the Fleiss-Cuzick estimator, the Pearson estimator, an estimator based on generalized estimating equations and an estimator from a random intercept logistic regression model. We compared estimates of the ICC for the overall sample and by study condition. Our results show that ICC estimates from different methods can be quite different, although confidence intervals generally overlap. The ICC varied substantially by study condition in two studies, suggesting that the common practice of assuming a common ICC across all clusters in the trial is questionable. A simulation study confirmed pitfalls of erroneously assuming a common ICC. Investigators should consider using sample size and analysis methods that allow the ICC to vary by study condition.

  16. Development of a quantum-dot-labelled magnetic immunoassay method for circulating colorectal cancer cell detection

    Institute of Scientific and Technical Information of China (English)

    Maria Gazouli; Anna Lyberopoulou; Pericles Pericleous; Spyros Rizos; Gerassimos Aravantinos; Nikolaos Nikiteas; Nicholas P Anagnou


    AIM:To detect of colorectal cancer (CRC) circulating tumour cells (CTCs) surface antigens,we present an assay incorporating cadmium selenide quantum dots (QDs) in these paper.METHODS:The principle of the assay is the immunomagnetic separation of CTCs from body fluids in conjunction with QDs,using specific antibody biomarkers:epithelial cell adhesion molecule antibody,and monoclonal cytokeratin 19 antibody.The detection signal was acquired from the fluorescence signal of QDs.For the evaluation of the performance,the method under study was used to isolate the human colon adenocarcinoma cell line (DLD-1) and CTCs from CRC patients' peripheral blood.RESULTS:The minimum detection limit of the assay was defined to 10 DLD-1 CRC cells/mL as fluorescence was measured with a spectrofluorometer.Fluorescenceactivated cell sorting analysis and Real Time RT-PCR,they both have also been used to evaluate the performance of the described method.In conclusion,we developed a simple,sensitive,efficient and of lower cost (than the existing ones) method for the detection of CRC CTCs in human samples.We have accomplished these results by using magnetic bead isolation and subsequent QD fluorescence detection.CONCLUSION:The method described here can be easily adjusted for any other protein target of either the CTC or the host.

  17. KRAS mutation analysis by PCR: a comparison of two methods.

    Directory of Open Access Journals (Sweden)

    Louise Bolton

    Full Text Available KRAS mutation assays are important companion diagnostic tests to guide anti-EGFR antibody treatment of metastatic colorectal cancer. Direct comparison of newer diagnostic methods with existing methods is an important part of validation of any new technique. In this this study, we have compared the Therascreen (Qiagen ARMS assay with Competitive Allele-Specific TaqMan PCR (castPCR, Life Technologies to determine equivalence for KRAS mutation analysis.DNA was extracted by Maxwell (Promega from 99 colorectal cancers. The ARMS-based Therascreen and a customized castPCR assay were performed according to the manufacturer's instructions. All assays were performed on either an Applied Biosystems 7500 Fast Dx or a ViiA7 real-time PCR machine (both from Life Technologies. The data were collected and discrepant results re-tested with newly extracted DNA from the same blocks in both assay types.Of the 99 tumors included, Therascreen showed 62 tumors to be wild-type (WT for KRAS, while 37 had KRAS mutations on initial testing. CastPCR showed 61 tumors to be wild-type (WT for KRAS, while 38 had KRAS mutations. Thirteen tumors showed BRAF mutation in castPCR and in one of these there was also a KRAS mutation. The custom castPCR plate included several other KRAS mutations and BRAF V600E, not included in Therascreen, explaining the higher number of mutations detected by castPCR. Re-testing of discrepant results was required in three tumors, all of which then achieved concordance for KRAS. CastPCR assay Ct values were on average 2 cycles lower than Therascreen.There was excellent correlation between the two methods. Although castPCR assay shows lower Ct values than Therascreen, this is unlikely to be clinically significant.

  18. Application of the rank-based method to DNA methylation for cancer diagnosis. (United States)

    Li, Hongdong; Hong, Guini; Xu, Hui; Guo, Zheng


    Detecting aberrant DNA methylation as diagnostic or prognostic biomarkers for cancer has been a topic of considerable interest recently. However, current classifiers based on absolute methylation values detected from a cohort of samples are typically difficult to be transferable to other cohorts of samples. Here, focusing on relative methylation levels, we employed a modified rank-based method to extract reversal pairs of CpG sites whose relative methylation level orderings differ between disease samples and normal controls for cancer diagnosis. The reversal pairs identified for five cancer types respectively show excellent prediction performance with the accuracy above 95%. Furthermore, when evaluating the reversal pairs identified for one cancer type in an independent cohorts of samples, we found that they could distinguish different subtypes of this cancer or different malignant stages including early stage of this cancer from normal controls. The identified reversal pairs also appear to be specific to cancer type. In conclusion, the reversal pairs detected by the rank-based method could be used for accurate cancer diagnosis, which are transferable to independent cohorts of samples.

  19. Impact of the Choice of Normalization Method on Molecular Cancer Class Discovery Using Nonnegative Matrix Factorization (United States)

    Yang, Haixuan; Seoighe, Cathal


    Nonnegative Matrix Factorization (NMF) has proved to be an effective method for unsupervised clustering analysis of gene expression data. By the nonnegativity constraint, NMF provides a decomposition of the data matrix into two matrices that have been used for clustering analysis. However, the decomposition is not unique. This allows different clustering results to be obtained, resulting in different interpretations of the decomposition. To alleviate this problem, some existing methods directly enforce uniqueness to some extent by adding regularization terms in the NMF objective function. Alternatively, various normalization methods have been applied to the factor matrices; however, the effects of the choice of normalization have not been carefully investigated. Here we investigate the performance of NMF for the task of cancer class discovery, under a wide range of normalization choices. After extensive evaluations, we observe that the maximum norm showed the best performance, although the maximum norm has not previously been used for NMF. Matlab codes are freely available from: PMID:27741311

  20. Prevalence of human papillomavirus in epithelial ovarian cancer tissue. A meta-analysis of observational studies

    DEFF Research Database (Denmark)

    Svahn, Malene F; Faber, Mette Tuxen; Christensen, Jane


    The role of human papillomavirus (HPV) in the pathogenesis of ovarian cancer is controversial, and conflicting results have been published. We conducted a systematic review and meta-analysis to estimate the prevalence of HPV in epithelial ovarian cancer tissue.......The role of human papillomavirus (HPV) in the pathogenesis of ovarian cancer is controversial, and conflicting results have been published. We conducted a systematic review and meta-analysis to estimate the prevalence of HPV in epithelial ovarian cancer tissue....

  1. A high-efficiency aerothermoelastic analysis method (United States)

    Wan, ZhiQiang; Wang, YaoKun; Liu, YunZhen; Yang, Chao


    In this paper, a high-efficiency aerothermoelastic analysis method based on unified hypersonic lifting surface theory is established. The method adopts a two-way coupling form that couples the structure, aerodynamic force, and aerodynamic thermo and heat conduction. The aerodynamic force is first calculated based on unified hypersonic lifting surface theory, and then the Eckert reference temperature method is used to solve the temperature field, where the transient heat conduction is solved using Fourier's law, and the modal method is used for the aeroelastic correction. Finally, flutter is analyzed based on the p-k method. The aerothermoelastic behavior of a typical hypersonic low-aspect ratio wing is then analyzed, and the results indicate the following: (1) the combined effects of the aerodynamic load and thermal load both deform the wing, which would increase if the flexibility, size, and flight time of the hypersonic aircraft increase; (2) the effect of heat accumulation should be noted, and therefore, the trajectory parameters should be considered in the design of hypersonic flight vehicles to avoid hazardous conditions, such as flutter.

  2. Control of data quality for population-based cancer survival analysis.


    Li, R.; Abela, L; Moore, J.; Woods, LM; Nur, U; Rachet, B; Allemani, C; Coleman, MP


    BACKGROUND: Population-based cancer survival is an important measure of the overall effectiveness of cancer care in a population. Population-based cancer registries collect data that enable the estimation of cancer survival. To ensure accurate, consistent and comparable survival estimates, strict control of data quality is required before the survival analyses are carried out. In this paper, we present a basis for data quality control for cancer survival. METHODS: We propose three distinct ph...

  3. Expression of tumor related gene NAG6 in gastric cancer and restriction fragment length polymorphism analysis

    Institute of Scientific and Technical Information of China (English)

    Xiao-Mei Zhang; Shou-Rong Sheng; Xiao-Yan Wang; Liang-Hua Bin; Jie-Ru Wang; Gui-Yuan Li


    AIM: NAG6 gene is a novel tumor related gene identified recently. This study was designed to examine the expression of this gene in gastric cancer and corresponding normal tissues, and to investigate its role in the occurrence and development of gastric cancer, also to study if the genetic structure of NAG6 was altered in gastric cancer.METHODS: Reverse transcription-polymerase chain reaction (RT-PCR), Northern blot analysis and dot hybridization were used to compare the expression level of NAG6 gene in 42cases of gastric cancer tissues with their corresponding normal tissues of the same patients respectively. In addition,restriction fragment length polymorphism (RFLP) analysis was adopted to study if the genetic structure of NAG6 was altered in gastric carcinomas.RESULTS: The expression of NAG6 in 57.1% gastric cancer tissues (25/42) was absent by RT-PCR analysis. The downregulation rate of NAG6 in gastric cancer tissues was significantly higher than that in corresponding normal tissues (P<0.01). However no correlation between the downregulation of NAG6 and lymph-node and/or distance metastasis was found in this study (P>0.05). Dot hybridization confirmed the results of RT-PCR. Furthermore,the results of EcoRI RFLP analysis of NAG6 gene demonstrated that 3 of 7 cases of gastric cancer showed loss of 5 kb fragment in comparison with their corresponding normal tissues.CONCLUSION: NAG6 gene is significantly down regulated in gastric cancer. The loss of genetic materials may be the cause of down-regulation of NAG6 expression. This seems to suggest that NAG6 may represent a candidate of putative tumor suppressor gene at 7q31-32 loci associated with gastric carcinoma. The down-regulation of this gene may play a role in occurrence and development of this disease, however it may not be associated with lymph node and/or distance metastasis.

  4. Prognostic Role of the Pretreatment C-Reactive Protein/Albumin Ratio in Solid Cancers: A Meta-Analysis (United States)

    Li, Nan; Tian, Guang-Wei; Wang, Ying; Zhang, Hui; Wang, Zi-hui; Li, Guang


    The C-reactive protein/albumin ratio (CAR) has been shown to play a significant prognostic role in several cancers. We aimed to comprehensively explore the potential role of the CAR as a prognostic indicator in solid cancers. In this meta-analysis, we collected data from 10 studies that examined the association between serum CAR and overall survival in patients with cancer. This meta-analysis included 4592 tumor patients. The eligible studies were found through the PubMed and Web of Science databases updated on 6 Oct 2016. The pooled hazard ratio (2.01, 95% CI: 1.58–2.56, p < 0.001) indicated that high CAR yielded worse survival in different cancers. Subgroup analyses showed a significant association between CAR and prognosis, regardless of the cutoff value, cutoff value selection, treatment method, country, sample size, stage and cancer type. This meta-analysis suggests that CAR may be a potential prognostic marker in solid cancers. However, further large prospective studies should be conducted to explore the critical role of CAR in survival of cancer patients. PMID:28128229

  5. Association between dietary vitamin C intake and risk of esophageal cancer: A dose-response meta-analysis. (United States)

    Bo, Yacong; Lu, Yan; Zhao, Yan; Zhao, Erjiang; Yuan, Ling; Lu, Weiquan; Cui, Lingling; Lu, Quanjun


    While several epidemiological studies have investigated the association between vitamin C and risk of esophageal cancer, the results remain inconsistent. In the present study, a meta-analysis was conducted to assess the impact of dietary vitamin C intake on esophageal cancer risk. Online databases were searched up to March 29, 2015, for studies on the association between dietary vitamin C intake and esophageal cancer risk. Pooled risk ratios (RRs) or odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using a random-effects model. Dose-response analyses were performed using the method of restricted cubic splines with four knots at percentiles of 5, 35, 65 and 95% of the distribution. Publication bias was estimated using Egger's tests and funnel plots. In all, 15 articles were included in this meta-analysis, including 20 studies, containing 7063 controls and 3955 cases of esophageal cancer. By comparing the highest vs. the lowest categories of vitamin C intake, we found that vitamin C was inversely associated with the risk of esophageal cancer [overall OR = 0.58, 95% CI = 0.49-0.68, I(2) = 56%]. A linear dose-response relationship was found. With an increase in dietary vitamin C intake of 50 mg/day, the risk of esophageal cancer statistically decreased by 13% (OR = 0.87, 95% CI = 0.80-0.93, p(linearity) = 0.0002). In conclusion, our analysis suggested that the higher intake of dietary vitamin C might have a protective effect against esophageal cancer.

  6. A comprehensive method for predicting fatal liver failure of patients with liver cancer resection. (United States)

    Li, Jiangfa; Lei, Biao; Nie, Xingju; Lin, Linku; Tahir, Syed Abdul; Shi, Wuxiang; Jin, Junfei; He, Songqing


    There are many methods to assess liver function, but none of them has been verified as fully effective. The purpose of this study is to establish a comprehensive method evaluating perioperative liver reserve function (LRF) in patients with primary liver cancer (PLC).In this study, 310 PLC patients who underwent liver resection were included. The cohort was divided into a training set (n = 235) and a validation set (n = 75). The factors affecting postoperative liver dysfunction (POLD) during preoperative, intraoperative, and postoperative periods were confirmed by logistic regression analysis. The equation for calculating the preoperative liver functional evaluation index (PLFEI) was established; the cutoff value of PLFEI determined through analysis by receiver-operating characteristic curve was used to predict postoperative liver function.The data showed that body mass index, international normalized ratio, indocyanine green (ICG) retention rate at 15 minutes (ICGR15), ICG elimination rate, standard remnant liver volume (SRLV), operative bleeding volume (OBV), blood transfusion volume, and operative time were statistically different (all P POLD. The relationship among PLFEI, ICGR15, OBV, and SRLV is expressed as an equation of "PLFEI = 0.181 × ICGR15 + 0.001 × OBV - 0.008 × SRLV." The cutoff value of PLFEI to predict POLD was -2.16 whose sensitivity and specificity were 90.3% and 73.5%, respectively. However, when predicting fatal liver failure (FLF), the cutoff value of PLFEI was switched to -1.97 whose sensitivity and specificity were 100% and 68.8%, respectively.PLFEI will be a more comprehensive, sensitive, and accurate index assessing perioperative LRF in liver cancer patients who receive liver resection. And keeping PLFEI <-1.97 is a safety margin for preventing FLF in PLC patients who underwent liver resection.

  7. Practical Method of Adaptive Radiotherapy for Prostate Cancer Using Real-Time Electromagnetic Tracking

    Energy Technology Data Exchange (ETDEWEB)

    Olsen, Jeffrey R.; Noel, Camille E.; Baker, Kenneth; Santanam, Lakshmi; Michalski, Jeff M. [Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO (United States); Parikh, Parag J., E-mail: [Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO (United States)


    Purpose: We have created an automated process using real-time tracking data to evaluate the adequacy of planning target volume (PTV) margins in prostate cancer, allowing a process of adaptive radiotherapy with minimal physician workload. We present an analysis of PTV adequacy and a proposed adaptive process. Methods and Materials: Tracking data were analyzed for 15 patients who underwent step-and-shoot multi-leaf collimation (SMLC) intensity-modulated radiation therapy (IMRT) with uniform 5-mm PTV margins for prostate cancer using the Calypso Registered-Sign Localization System. Additional plans were generated with 0- and 3-mm margins. A custom software application using the planned dose distribution and structure location from computed tomography (CT) simulation was developed to evaluate the dosimetric impact to the target due to motion. The dose delivered to the prostate was calculated for the initial three, five, and 10 fractions, and for the entire treatment. Treatment was accepted as adequate if the minimum delivered prostate dose (D{sub min}) was at least 98% of the planned D{sub min}. Results: For 0-, 3-, and 5-mm PTV margins, adequate treatment was obtained in 3 of 15, 12 of 15, and 15 of 15 patients, and the delivered D{sub min} ranged from 78% to 99%, 96% to 100%, and 99% to 100% of the planned D{sub min}. Changes in D{sub min} did not correlate with magnitude of prostate motion. Treatment adequacy during the first 10 fractions predicted sufficient dose delivery for the entire treatment for all patients and margins. Conclusions: Our adaptive process successfully used real-time tracking data to predict the need for PTV modifications, without the added burden of physician contouring and image analysis. Our methods are applicable to other uses of real-time tracking, including hypofractionated treatment.

  8. Homemade oral supplements for patients with cancer: descriptive analysis


    Garófolo,Adriana; Alves,Fernanda Rodrigues; Rezende, Maria Aurelia do Carmo


    ObjectiveThis study aimed to describe the development of eight formulations of homemade oral supplements that propose to increase the energy, protein and micronutrient intakes of patients with cancer, analyze its nutritional value and assess its taste using two different fat sources.MethodsThe supplements were based on four ingredients: milk, eggs, sugars and oils for nutritional recovery. the formulations were calculated by the nutritional support software NUTWIN. the nutritional value of th...

  9. Smokeless Tobacco and Oral Cancer in South Asia: A Systematic Review with Meta-Analysis

    Directory of Open Access Journals (Sweden)

    Zohaib Khan


    Full Text Available Introduction. Smokeless tobacco is considered one of the major risk factors for oral cancer. It is estimated that over 90% of the global smokeless tobacco use burden is in South Asia. This paper aims to systematically review publications reporting epidemiological observational studies published in South Asia from 1984 till 2013. Methods. An electronic search in “Medline” and “ISI Web of Knowledge” yielded 734 publications out of which 21 were included in this review. All publications were assessed for quality using a standard quality assessment tool. Effect estimates (odds ratios (OR were abstracted or calculated from the given data. A random effects meta-analysis was performed to assess the risk of oral cancer with the use of different forms of smokeless tobacco. Results and Conclusion. The pooled OR for chewing tobacco and risk of oral cancer was 4.7 [3.1–7.1] and for paan with tobacco and risk of oral cancer was 7.1 [4.5–11.1]. The findings of this study suggest a strong causal link between oral cancer and various forms of smokeless tobacco. Public health policies in affected countries should consider SLT specific cessation programs in addition to campaigns and activities incorporated into smoking cessation programs.

  10. Survival analysis of colorectal cancer patients with tumor recurrence using global score test methodology

    Energy Technology Data Exchange (ETDEWEB)

    Zain, Zakiyah, E-mail:; Ahmad, Yuhaniz, E-mail: [School of Quantitative Sciences, Universiti Utara Malaysia, UUM Sintok 06010, Kedah (Malaysia); Azwan, Zairul, E-mail:, E-mail:, E-mail:; Raduan, Farhana, E-mail:, E-mail:, E-mail:; Sagap, Ismail, E-mail:, E-mail:, E-mail: [Surgery Department, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, 56000 Bandar Tun Razak, Kuala Lumpur (Malaysia); Aziz, Nazrina, E-mail:


    Colorectal cancer is the third and the second most common cancer worldwide in men and women respectively, and the second in Malaysia for both genders. Surgery, chemotherapy and radiotherapy are among the options available for treatment of patients with colorectal cancer. In clinical trials, the main purpose is often to compare efficacy between experimental and control treatments. Treatment comparisons often involve several responses or endpoints, and this situation complicates the analysis. In the case of colorectal cancer, sets of responses concerned with survival times include: times from tumor removal until the first, the second and the third tumor recurrences, and time to death. For a patient, the time to recurrence is correlated to the overall survival. In this study, global score test methodology is used in combining the univariate score statistics for comparing treatments with respect to each survival endpoint into a single statistic. The data of tumor recurrence and overall survival of colorectal cancer patients are taken from a Malaysian hospital. The results are found to be similar to those computed using the established Wei, Lin and Weissfeld method. Key factors such as ethnic, gender, age and stage at diagnose are also reported.

  11. Methods and rationale used in a matched cohort study of the incidence of new primary cancers following prostate cancer

    Directory of Open Access Journals (Sweden)

    Cronin-Fenton DP


    Full Text Available Deirdre P Cronin-Fenton,1 Sussie Antonsen,1 Karynsa Cetin,2 John Acquavella,2 Andre Daniels,3 Timothy L Lash1,4 1Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, Denmark; 2Center for Observational Research, Amgen Incorporated, Thousand Oaks, CA, USA; 3Global Regulatory Affairs and Safety, Amgen Incorporated, Thousand Oaks, CA, USA; 4Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA Objectives: We describe several methodological issues that were addressed in conducting a Danish population-based matched cohort study comparing rates of new primary cancers (NPCs in men with and without prostate cancer (PC. Methods: We matched 30,220 men with PC to 151,100 men without PC (comparators on age (±2 years and PC diagnosis/index date. We focused on several methodological issues: 1 to address survival differences between the cohorts we compared rates with and without censoring comparators on the date their matched PC patient died or was censored; 2 to address diagnostic bias, we excluded men with a history of cancer from the comparator cohort; 3 to address prostate cancer immunity, we graphed the hazard of NPC in both cohorts, with and without prostate cancer as an outcome; 4 we used empirical Bayes methods to explore the effect of adjusting for multiple comparisons. Results: After 18 months of follow-up, cumulative person-time was lower in the PC than comparator cohort due to higher mortality among PC patients. Terminating person-time in comparators at the matched PC patient's death or loss to follow-up resulted in comparable person-time up to 30 months of follow-up and lower person-time among comparators thereafter. The hazard of NPC was lower among men with PC than comparators throughout follow-up. There was little difference in rates beyond the first four years of follow-up after removing PC as an outcome. Empirical Bayes adjustment for multiple comparisons had little effect on the

  12. Prognostic value of CD166 expression in cancers of the digestive system: a systematic review and meta-analysis.

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    Chao Ni

    Full Text Available OBJECTIVE: Many studies have reported the prognostic predictive value of CD166 as a cancer stem cell marker in cancers of the digestive system; however, its predictive value remains controversial. Here, we investigate the correlation between CD166 positivity in digestive system cancers and clinicopathological features using meta-analysis. METHODS: A comprehensive search in PubMed and ISI Web of Science through March of 2013 was performed. Only articles containing CD166 antigen immunohistochemical staining in cancers of the digestive system were included,including pancreatic cancer, esophageal cancer, gastric cancer and colorectal cancer. Data comparing 3- and 5-year overall survival along with other clinicopathological features were collected. RESULTS: Nine studies with 2553 patients who met the inclusion criteria were included for the analysis. The median rate of CD166 immunohistochemical staining expression was 56% (25.4%-76.3%. In colorectal cancer specifically, the results of a fixed-effects model indicated that CD166-positive expression was an independent marker associated with a smaller tumor burden (T category; RR = 0.93, 95%, CI: 0.88-0.98 but worse spread to nearby lymph nodes (N category; RR = 1.17, 95% CI: 1.05-1.30. The 5-year overall survival rate was showed relationship with cytoplasmic positive staining of CD166 (RR = 1.47 95% 1.21-1.79, but no significant association was found in the pool or any other stratified analysis with 3- or 5- year overall survival rate. CONCLUSION: Based on the published studies, different cellular location of CD166 has distinct prognostic value and cytoplasmic positive expression is associated with worse prognosis outcome. Besides, our results also find CD166 expression indicate advanced T category and N-positive status in colorectal cancer specifically.

  13. Chemotherapy versus support cancer treatment in advanced gastric cancer: a meta-analysis

    Directory of Open Access Journals (Sweden)

    L. Casaretto


    Full Text Available The aim of the present study was to compare the efficacy of chemotherapy and support treatment in patients with advanced non-resectable gastric cancer in a systematic review and meta-analysis of randomized clinical trials that included a comparison of chemotherapy and support care treatment in patients diagnosed with gastric adenocarcinoma, regardless of their age, gender or place of treatment. The search strategy was based on the criteria of the Cochrane Base, using the following key words: 1 randomized clinical trials and antineoplastic combined therapy or gastrointestinal neoplasm, 2 stomach neoplasm and drug therapy, 3 clinical trial and multi-modality therapy, 4 stomach neoplasm and drug therapy or quality of life, 5 double-blind method or clinical trial. The search was carried out using the Cochrane, Medline and Lilacs databases. Five studies fulfilled the inclusion criteria, for a total of 390 participants, 208 (53% receiving chemotherapy, 182 (47% receiving support care treatment and 6 losses (1.6%. The 1-year survival rate was 8% for support care and 20% for chemotherapy (RR = 2.14, 95% CI = 1.00-4.57, P = 0.05; 30% of the patients in the chemotherapy group and 12% in the support care group attained a 6-month symptom-free period (RR = 2.33, 95% CI = 1.41-3.87, P < 0.01. Quality of life evaluated after 4 months was significantly better for the chemotherapy patients (34%; RR = 2.07, 95% CI = 1.31-3.28, P < 0.01 with tumor mass reduction (RR = 3.32, 95% CI = 0.77-14.24, P = 0.1. Chemotherapy increased the 1-year survival rate of the patients and provided a longer symptom-free period of 6 months and an improvement in quality of life.

  14. Lung cancer associated hypercalcemia: An analysis of factors influencing survival and prognosis in 34 cases

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    Su-jie ZHANG


    Full Text Available Objectives  To explore the factors influencing survival time in lung cancer associated hypercalcemia patients. Methods  Thirty-four patients with pathologically confirmed lung cancer complicated with hypercalcemia, who were treated at the Department of Oncology in General Hospital of PLA from Jan. 2001 to Dec. 2010, were enrolled in this study. The clinical data analyzed included sex, age, pathological type of the malignancies, organ metastasis (bone, lung, liver, kidney, brain, number of distal metastatic site, mental status, interval between final diagnosis of lung cancer and of hypercalcemia, peak value of blood calcium during the disease course, treatment methods and so on. Survival analysis was performed with the Kaplan-Meier method and Cox analysis with statistic software SPSS 18.0 to identify the potential prognostic factors. Results  The highest blood calcium level ranged from 2.77 to 4.87mmol/L, and the median value was 2.94mmol/L. The patients' survival time after diagnosis of hypercalcemia varied from 1 day to 1067 days, and the median survival time was 92 days. With the log-rank test, age above 50 years old, hypercalcemia occurring over 90 days after diagnosis of cancer, central nervous system symptoms and renal metastasis were predictors for poor survival (P=0.048, P=0.001, P=0.000, P=0.003. In the COX proportional hazard model analysis, age above 50 years old, hypercalcemia occurring over 90 days after cancer diagnosis, central nervous system symptoms and renal metastasis were significant prognostic factors for poor survival (HR=11.483, P=0.006; HR=4.371, P=0.002; HR=6.064, P=0.026; HR=8.502, P=0.011. Conclusions  Patients with lung cancer associated hypercalcemia have a shorter survival time and poor prognosis. Age above 50 years old, hypercalcemia occurring over 90 days after cancer diagnosis, central nervous system symptoms and renal metastasis are significant factors of poor prognosis.

  15. Identification of Personalized Chemoresistance Genes in Subtypes of Basal-Like Breast Cancer Based on Functional Differences Using Pathway Analysis.

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    Tong Wu

    Full Text Available Breast cancer is a highly heterogeneous disease that is clinically classified into several subtypes. Among these subtypes, basal-like breast cancer largely overlaps with triple-negative breast cancer (TNBC, and these two groups are generally studied together as a single entity. Differences in the molecular makeup of breast cancers can result in different treatment strategies and prognoses for patients with different breast cancer subtypes. Compared with other subtypes, basal-like and other ER+ breast cancer subtypes exhibit marked differences in etiologic factors, clinical characteristics and therapeutic potential. Anthracycline drugs are typically used as the first-line clinical treatment for basal-like breast cancer subtypes. However, certain patients develop drug resistance following chemotherapy, which can lead to disease relapse and death. Even among patients with basal-like breast cancer, there can be significant molecular differences, and it is difficult to identify specific drug resistance proteins in any given patient using conventional variance testing methods. Therefore, we designed a new method for identifying drug resistance genes. Subgroups, personalized biomarkers, and therapy targets were identified using cluster analysis of differentially expressed genes. We found that basal-like breast cancer could be further divided into at least four distinct subgroups, including two groups at risk for drug resistance and two groups characterized by sensitivity to pharmacotherapy. Based on functional differences among these subgroups, we identified nine biomarkers related to drug resistance: SYK, LCK, GAB2, PAWR, PPARG, MDFI, ZAP70, CIITA and ACTA1. Finally, based on the deviation scores of the examined pathways, 16 pathways were shown to exhibit varying degrees of abnormality in the various subgroups, indicating that patients with different subtypes of basal-like breast cancer can be characterized by differences in the functional status of

  16. Thermal Analysis Methods for Aerobraking Heating (United States)

    Amundsen, Ruth M.; Gasbarre, Joseph F.; Dec, John A.


    As NASA begins exploration of other planets, a method of non-propulsively slowing vehicles at the planet, aerobraking, may become a valuable technique for managing vehicle design mass and propellant. An example of this is Mars Reconnaissance Orbiter (MRO), which will launch in late 2005 and reach Mars in March of 2006. In order to save propellant, MRO will use aerobraking to modify the initial orbit at Mars. The spacecraft will dip into the atmosphere briefly on each orbit, and during the drag pass, the atmospheric drag on the spacecraft will slow it, thus lowering the orbit apoapsis. The largest area on the spacecraft, and that most affected by the heat generated during the aerobraking process, is the solar arrays. A thermal analysis of the solar arrays was conducted at NASA Langley, to simulate their performance throughout the entire roughly 6-month period of aerobraking. Several interesting methods were used to make this analysis more rapid and robust. Two separate models were built for this analysis, one in Thermal Desktop for radiation and orbital heating analysis, and one in MSC.Patran for thermal analysis. The results from the radiation model were mapped in an automated fashion to the Patran thermal model that was used to analyze the thermal behavior during the drag pass. A high degree of automation in file manipulation as well as other methods for reducing run time were employed, since toward the end of the aerobraking period the orbit period is short, and in order to support flight operations the runs must be computed rapidly. All heating within the Patran Thermal model was combined in one section of logic, such that data mapped from the radiation model and aeroheating model, as well as skin temperature effects on the aeroheating and surface radiation, could be incorporated easily. This approach calculates the aeroheating at any given node, based on its position and temperature as well as the density and velocity at that trajectory point. Run times on

  17. Digital methods for mediated discourse analysis

    DEFF Research Database (Denmark)

    Kjær, Malene; Larsen, Malene Charlotte


    , restrictions or privately mediated settings. Having used mediated discourse analysis (Scollon 2002, Scollon & Scollon, 2004) as a framework in two different research projects, we show how the framework, in correlation with digital resources for data gathering, provides new understandings of 1) the daily...... practice of health care professionals (Author 1, 2014) and 2) young people’s identity construction on social media platforms (Author 2, 2010, 2015, in press). The paper’s contribution is a methodological discussion on digital data collection using methods such as online interviewing (via e-mail or chat......) and online questionnaire data in order to capture mediated actions and discourses in practice....

  18. Numerical analysis method for linear induction machines. (United States)

    Elliott, D. G.


    A numerical analysis method has been developed for linear induction machines such as liquid metal MHD pumps and generators and linear motors. Arbitrary phase currents or voltages can be specified and the moving conductor can have arbitrary velocity and conductivity variations from point to point. The moving conductor is divided into a mesh and coefficients are calculated for the voltage induced at each mesh point by unit current at every other mesh point. Combining the coefficients with the mesh resistances yields a set of simultaneous equations which are solved for the unknown currents.


    Institute of Scientific and Technical Information of China (English)


    The greatest benefit is realized from failure mode, effect and criticality analysis (FMECA) when it is done early in the design phase and tracks product changes as they evolve; design changes can then be made more economically than if the problems are discovered after the design has been completed. However, when the discovered design flaws must be prioritized for corrective actions, precise information on their probability of occurrence, the effect of the failure, and their detectability often are not availabe. To solve this problem, this paper described a new method, based on fuzzy sets, for prioritizing failures for corrective actions in a FMCEA. Its successful application to the container crane shows that the proposed method is both reasonable and practical.


    Directory of Open Access Journals (Sweden)

    Priya Antony.P


    Full Text Available Cancer is a leading cause of death worldwide and it is characterized by uncontrolled growth of cells in the body. Apoptosis or programmed cell death plays a major role in normal cell development and tissue homeostasis and cancer cells do lack this property. The Bcl-2 family of proteins regulates apoptotic pathway by the interaction of pro apoptotic and anti apoptotic proteins. They maintain a balance between newly forming cells and old dying cells. Over expressed anti apoptotic Bcl-2 will alter the ratio of pro and anti apoptotic proteins, resulting in the prevention of apoptosis. Elevated levels of apoptosis-inhibitory protein Bcl-2 has frequently been detected in many forms of human cancer. Therefore, Bcl-2 appears to be a relevant target for cancer therapy. Plants have been used for treating various diseases since ancient times. Boerhaavia diffusa is an important medicinal plant used in various human ailments, including cancer, diabetes, hepatoprotective and anti-inflammatory effects. However, most of the reports in traditional medicine are yet to be validated through scientific studies. The present study focuses on identifying phytocompounds in Boerhaavia diffusa having anticancer potential to effectively inhibit the action of Bcl- 2 protein. Insilico docking analysis are well adapted for screening of phytocompounds so as to find the inhibitory or promotive role of potent lead molecules against respective targets. Thirty seven ligands of various confirmations were docked to target protein Bcl-2 using Discovery studio 3.5. The most effective ones were identified through docking score and interaction energy.

  1. Colorectal cancer association with metabolic syndrome and its components: a systematic review with meta-analysis. (United States)

    Esposito, Katherine; Chiodini, Paolo; Capuano, Annalisa; Bellastella, Giuseppe; Maiorino, Maria Ida; Rafaniello, Concetta; Panagiotakos, Demosthenes B; Giugliano, Dario


    We performed a systematic review and meta-analysis of the empirical evidence on the association of metabolic syndrome and its components with colorectal cancer incidence and mortality. A systematic literature search of multiple electronic databases was conducted and complemented by cross-referencing to identify studies published before 31 October 2012. Every included study was to report risk estimates with 95 % confidence intervals for the association between metabolic syndrome and colorectal cancer (incidence or mortality). Core items of identified studies were independently extracted by two reviewers, and results were summarized by standard methods of meta-analysis. We identified 17 studies, which reported on 49 data sets with 11,462 cancer cases. Metabolic syndrome was associated with an increased risk of colorectal cancer incidence and mortality in both men (RR: 1.33, 95 % CI 1.18-1.50, and 1.36, 1.25-1.48, respectively) and women (RR: 1.41, 1.18-1.70, and 1.16, 1.03-1.30, respectively). The risk estimates changed little depending on type of study (cohort vs non cohort), populations (US, Europe, Asia), cancer site (colon and rectum), or definition of the syndrome. The risk estimates for any single factor of the syndrome were significant for higher values of BMI/waist (RR: 1.19, 95 % CI 1.10-1.28), dysglycemia (RR: 1.29, 1.11-1.49), and higher blood pressure (RR: 1.09, 1.01-1.18). Dysglycemia and/or higher BMI/waist explained most of the risk associated with metabolic syndrome. Metabolic syndrome is associated with an increased risk of colorectal cancer incidence and mortality in both sexes. The risk conveyed by the full syndrome is not superior to the sum of its parts.

  2. Association between the CYP1B1 polymorphisms and risk of cancer: a meta-analysis. (United States)

    Liu, Jie-Ying; Yang, Yu; Liu, Zhi-Zhong; Xie, Jian-Jun; Du, Ya-Ping; Wang, Wei


    The previous, published data on the association between CYP1B1 polymorphisms and cancer risk remained controversial. To derive a more precise estimation of the association between the CYP1B1 polymorphisms and cancer risk, we performed a meta-analysis to investigate the association between cancer susceptibility and CYP1B1 Leu432Val, Asn453Ser, Arg48Gly, and Ala119Ser polymorphisms. For Asn453Ser and Arg48Gly polymorphisms, significantly decreased endometrial cancer was observed among Caucasians. For Ala119Ser polymorphism, we found that individuals with the minor variant genotypes had a high risk of prostate cancer. For Leu432Val polymorphism, we found that individuals with the minor variant genotypes had a higher risk of endometrial cancer and lung cancer and had a lower risk of ovarian cancer. In summary, this meta-analysis suggests that Leu432Val polymorphism is associated with ovarian cancer, lung cancer, and endometrial cancer risk; Asn453Ser and Arg48Gly polymorphisms are associated with endometrial cancer risk among Caucasians, Ala119Ser polymorphism is associated with prostate cancer risk, and Ala119Ser polymorphism is associated with breast cancer risk in Caucasians. In addition, our work also points out the importance of new studies for Ala119Ser polymorphism in endometrial cancer, because high heterogeneity was observed (I (2) > 75 %).

  3. Proteomics Analysis of Ovarian Cancer Cell Lines and Tissues Reveals Drug Resistance-associated Proteins (United States)



    Background: Carboplatin and paclitaxel form the cornerstone of chemotherapy for epithelial ovarian cancer, however, drug resistance to these agents continues to present challenges. Despite extensive research, the mechanisms underlying this resistance remain unclear. Materials and Methods: A 2D-gel proteomics method was used to analyze protein expression levels of three human ovarian cancer cell lines and five biopsy samples. Representative proteins identified were validated via western immunoblotting. Ingenuity pathway analysis revealed metabolomic pathway changes. Results: A total of 189 proteins were identified with restricted criteria. Combined treatment targeting the proteasome-ubiquitin pathway resulted in re-sensitisation of drug-resistant cells. In addition, examination of five surgical biopsies of ovarian tissues revealed α-enolase (ENOA), elongation factor Tu, mitochondrial (EFTU), glyceraldehyde-3-phosphate dehydrogenase (G3P), stress-70 protein, mitochondrial (GRP75), apolipoprotein A-1 (APOA1), peroxiredoxin (PRDX2) and annexin A (ANXA) as candidate biomarkers of drug-resistant disease. Conclusion: Proteomics combined with pathway analysis provided information for an effective combined treatment approach overcoming drug resistance. Analysis of cell lines and tissues revealed potential prognostic biomarkers for ovarian cancer. *These Authors contributed equally to this study. PMID:28031236

  4. The insulin-like growth factor system is modulated by exercise in breast cancer survivors: a systematic review and meta-analysis


    Meneses-Echávez, José Francisco; Jiménez, Emilio González; Río-Valle, Jacqueline Schmidt; Correa-Bautista, Jorge Enrique; Izquierdo, Mikel; Ramírez-Vélez, Robinson


    Background Insulin-like growth factors (IGF´s) play a crucial role in controlling cancer cell proliferation, differentiation and apoptosis. Exercise has been postulated as an effective intervention in improving cancer-related outcomes and survival, although its effects on IGF´s are not well understood. This meta-analysis aimed to determine the effects of exercise in modulating IGF´s system in breast cancer survivors. Methods Databases of PuMed, EMBASE, Cochrane Central Register of Controlled ...

  5. Esophageal cancer metabolite biomarkers detected by LC-MS and NMR methods.

    Directory of Open Access Journals (Sweden)

    Jian Zhang

    Full Text Available BACKGROUND: Esophageal adenocarcinoma (EAC is a rarely curable disease and is rapidly rising worldwide in incidence. Barret's esophagus (BE and high-grade dysplasia (HGD are considered major risk factors for invasive adenocarcinoma. In the current study, unbiased global metabolic profiling methods were applied to serum samples from patients with EAC, BE and HGD, and healthy individuals, in order to identify metabolite based biomarkers associated with the early stages of EAC with the goal of improving prognostication. METHODOLOGY/PRINCIPAL FINDINGS: Serum metabolite profiles from patients with EAC (n = 67, BE (n = 3, HGD (n = 9 and healthy volunteers (n = 34 were obtained using high performance liquid chromatography-mass spectrometry (LC-MS methods. Twelve metabolites differed significantly (p<0.05 between EAC patients and healthy controls. A partial least-squares discriminant analysis (PLS-DA model had good accuracy with the area under the receiver operative characteristic curve (AUROC of 0.82. However, when the results of LC-MS were combined with 8 metabolites detected by nuclear magnetic resonance (NMR in a previous study, the combination of NMR and MS detected metabolites provided a much superior performance, with AUROC = 0.95. Further, mean values of 12 of these metabolites varied consistently from healthy controls to the high-risk individuals (BE and HGD patients and EAC subjects. Altered metabolic pathways including a number of amino acid pathways and energy metabolism were identified based on altered levels of numerous metabolites. CONCLUSIONS/SIGNIFICANCE: Metabolic profiles derived from the combination of LC-MS and NMR methods readily distinguish EAC patients and potentially promise important routes to understanding the carcinogenesis and detecting the cancer. Differences in the metabolic profiles between high-risk individuals and the EAC indicate the possibility of identifying the patients at risk much earlier to

  6. BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes. (United States)

    de Santiago, Ines; Liu, Wei; Yuan, Ke; O'Reilly, Martin; Chilamakuri, Chandra Sekhar Reddy; Ponder, Bruce A J; Meyer, Kerstin B; Markowetz, Florian


    Allele-specific measurements of transcription factor binding from ChIP-seq data are key to dissecting the allelic effects of non-coding variants and their contribution to phenotypic diversity. However, most methods of detecting an allelic imbalance assume diploid genomes. This assumption severely limits their applicability to cancer samples with frequent DNA copy-number changes. Here we present a Bayesian statistical approach called BaalChIP to correct for the effect of background allele frequency on the observed ChIP-seq read counts. BaalChIP allows the joint analysis of multiple ChIP-seq samples across a single variant and outperforms competing approaches in simulations. Using 548 ENCODE ChIP-seq and six targeted FAIRE-seq samples, we show that BaalChIP effectively corrects allele-specific analysis for copy-number variation and increases the power to detect putative cis-acting regulatory variants in cancer genomes.

  7. Anthropometric Factors and Thyroid Cancer Risk by Histological Subtype: Pooled Analysis of 22 Prospective Studies (United States)

    McCullough, Marjorie L.; Franceschi, Silvia; Rinaldi, Sabina; Wolk, Alicja; Neta, Gila; Olov Adami, Hans; Anderson, Kristin; Andreotti, Gabriella; Beane Freeman, Laura E.; Bernstein, Leslie; Buring, Julie E.; Clavel-Chapelon, Francoise; De Roo, Lisa A.; Gao, Yu-Tang; Gaziano, J. Michael; Giles, Graham G.; Håkansson, Niclas; Horn-Ross, Pamela L.; Kirsh, Vicki A.; Linet, Martha S.; MacInnis, Robert J.; Orsini, Nicola; Park, Yikyung; Patel, Alpa V.; Purdue, Mark P.; Riboli, Elio; Robien, Kimberly; Rohan, Thomas; Sandler, Dale P.; Schairer, Catherine; Schneider, Arthur B.; Sesso, Howard D.; Shu, Xiao-Ou; Singh, Pramil N.; van den Brandt, Piet A.; Ward, Elizabeth; Weiderpass, Elisabete; White, Emily; Xiang, Yong-Bing; Zeleniuch-Jacquotte, Anne; Zheng, Wei; Hartge, Patricia; Berrington de González, Amy


    Background: Greater height and body mass index (BMI) have been associated with an increased risk of thyroid cancer, particularly papillary carcinoma, the most common and least aggressive subtype. Few studies have evaluated these associations in relation to other, more aggressive histologic types or thyroid cancer-specific mortality. Methods: This large pooled analysis of 22 prospective studies (833,176 men and 1,260,871 women) investigated thyroid cancer incidence associated with greater height, BMI at baseline and young adulthood, and adulthood BMI gain (difference between young-adult and baseline BMI), overall and separately by sex and histological subtype using multivariable Cox proportional hazards regression models. Associations with thyroid cancer mortality were investigated in a subset of cohorts (578,922 men and 774,373 women) that contributed cause of death information. Results: During follow-up, 2996 incident thyroid cancers and 104 thyroid cancer deaths were identified. All anthropometric factors were positively associated with thyroid cancer incidence: hazard ratios (HR) [confidence intervals (CIs)] for height (per 5 cm) = 1.07 [1.04–1.10], BMI (per 5 kg/m2) = 1.06 [1.02–1.10], waist circumference (per 5 cm) = 1.03 [1.01–1.05], young-adult BMI (per 5 kg/m2) = 1.13 [1.02–1.25], and adulthood BMI gain (per 5 kg/m2) = 1.07 [1.00–1.15]. Associations for baseline BMI and waist circumference were attenuated after mutual adjustment. Baseline BMI was more strongly associated with risk in men compared with women (p = 0.04). Positive associations were observed for papillary, follicular, and anaplastic, but not medullary, thyroid carcinomas. Similar, but stronger, associations were observed for thyroid cancer mortality. Conclusion: The results suggest that greater height and excess adiposity throughout adulthood are associated with higher incidence of most major types of thyroid cancer, including the least common but

  8. Forecasting Age-Specific Brain Cancer Mortality Rates Using Functional Data Analysis Models

    Directory of Open Access Journals (Sweden)

    Keshav P. Pokhrel


    Full Text Available Incidence and mortality rates are considered as a guideline for planning public health strategies and allocating resources. We apply functional data analysis techniques to model age-specific brain cancer mortality trend and forecast entire age-specific functions using exponential smoothing state-space models. The age-specific mortality curves are decomposed using principal component analysis and fit functional time series model with basis functions. Nonparametric smoothing methods are used to mitigate the existing randomness in the observed data. We use functional time series model on age-specific brain cancer mortality rates and forecast mortality curves with prediction intervals using exponential smoothing state-space model. We also present a disparity of brain cancer mortality rates among the age groups together with the rate of change of mortality rates. The data were obtained from the Surveillance, Epidemiology and End Results (SEER program of the United States. The brain cancer mortality rates, classified under International Classification Disease code ICD-O-3, were extracted from SEER*Stat software.

  9. The benchmark analysis of gastric, colorectal and rectal cancer pathways: toward establishing standardized clinical pathway in the cancer care. (United States)

    Ryu, Munemasa; Hamano, Masaaki; Nakagawara, Akira; Shinoda, Masayuki; Shimizu, Hideaki; Miura, Takeshi; Yoshida, Isao; Nemoto, Atsushi; Yoshikawa, Aki


    Most clinical pathways in treating cancers in Japan are based on individual physician's personal experiences rather than on an empirical analysis of clinical data such as benchmark comparison with other hospitals. Therefore, these pathways are far from being standardized. By comparing detailed clinical data from five cancer centers, we have observed various differences among hospitals. By conducting benchmark analyses, providing detailed feedback to the participating hospitals and by repeating the benchmark a year later, we strive to develop more standardized clinical pathways for the treatment of cancers. The Cancer Quality Initiative was launched in 2007 by five cancer centers. Using diagnosis procedure combination data, the member hospitals benchmarked their pre-operative and post-operative length of stays, the duration of antibiotics administrations and the post-operative fasting duration for gastric, colon and rectal cancers. The benchmark was conducted by disclosing hospital identities and performed using 2007 and 2008 data. In the 2007 benchmark, substantial differences were shown among five hospitals in the treatment of gastric, colon and rectal cancers. After providing the 2007 results to the participating hospitals and organizing several brainstorming discussions, significant improvements were observed in the 2008 data study. The benchmark analysis of clinical data is extremely useful in promoting more standardized care and, thus in improving the quality of cancer treatment in Japan. By repeating the benchmark analyses, we can offer truly clinical evidence-based higher quality standardized cancer treatment to our patients.

  10. Tubal sterilization and breast cancer incidence: results from the cancer prevention study II nutrition cohort and meta-analysis. (United States)

    Gaudet, Mia M; Patel, Alpa V; Sun, Juzhong; Teras, Lauren R; Gapstur, Susan M


    Tubal sterilization is a common form of contraception in the United States and is hypothesized to be associated with a lower risk of breast cancer. However, prior observational studies have reported inconsistent results. We investigated the association between tubal sterilization and breast cancer risk among 77,249 postmenopausal, cancer-free women in the Cancer Prevention Study II (CPS-II) Nutrition Cohort, enrolled in 21 states in the United States during 1992-1993. During 15 years of follow-up through June 30, 2007, 4,084 invasive breast cancer cases were diagnosed. Multivariable Cox proportional hazard regression was used to estimate hazard ratios and 95% confidence intervals. A meta-analysis including the CPS-II Nutrition Cohort results with other published results from 4 case-control studies and 3 prospective studies was conducted to provide a summary estimate for the association between tubal sterilization and breast cancer risk. In the CPS-II Nutrition Cohort, tubal sterilization was not associated with breast cancer incidence (multivariable-adjusted hazard ratio = 1.08, 95% confidence interval: 0.97, 1.20). Associations stratified by year of tubal sterilization, age, and time since surgery were also null. The meta-analysis also found no association between tubal sterilization and breast cancer risk (odds ratio = 0.97, 95% confidence interval: 0.84, 1.09). Tubal sterilization does not appear to be associated with breast cancer risk.

  11. Vitamin D status and the risk of pancreatic cancer: a meta-analysis

    Institute of Scientific and Technical Information of China (English)

    LIU Shang-long; ZHAO Yu-pei; DAI Meng-hua; YOU Lei; WEN Zhang; XU Jian-wei


    Background Vitamin D status in relation to pancreatic cancer risks is still inconsistent.This study was performed to evaluate the association between vitamin D status and risk of pancreatic cancer using a meta-analysis approach.Methods A systemic review of all relevant literature in English was performed by searching Pubmed,Web of Science and Embase to identify eligible studies from the earliest available date to April 1,2012.The search terms "vitamin D","25-hydroxyvitamin D","pancreatic cancer" or "pancreatic neoplasms" were used to retrieve relevant papers.Inclusion criteria were:(1) the exposure of interest was intake of vitamin D or blood levels of vitamin D; (2) the outcome of interest was pancreatic cancer; (3) data on high and low intake or blood vitamin D in cases and controls were available; (4) odds ratio (OR) estimates with 95% confidence interval (C/) were provided; (5) primary epidemiological data were provided reporting pancreatic cancer incidence.The combined OR values and their 95% C/s were calculated via a meta-analysis.The potential presence of publication bias was estimated using Egger's regression asymmetry test.Results Nine studies with a total of 1 206 011 participants met the inclusion criteria.The test for heterogeneity showed there were significant differences among the included studies (l2=70.9%,P=0.001),so a randomized-effects model was used in the meta-analysis.The pooled OR of pancreatic cancer for the highest versus the lowest categories of vitamin D level was 1.14 (95% C/ 0.896-1.451),and the Z-score for the overall effect was 1.06 (P=0.288),showing that there was no significant association between vitamin D levels and the risk of pancreatic cancer.Egger's test indicated there was a low possibility of publication bias in this study (P=0.348).Conclusion Dietary vitamin D or circulating concentrations of 25-hydroxyvitamin D are not associated with the risk of pancreatic cancer based on evidence from currently published studies.

  12. Cross-Cancer Genome-Wide Analysis of Lung, Ovary, Breast, Prostate, and Colorectal Cancer Reveals Novel Pleiotropic Associations. (United States)

    Fehringer, Gordon; Kraft, Peter; Pharoah, Paul D; Eeles, Rosalind A; Chatterjee, Nilanjan; Schumacher, Fredrick R; Schildkraut, Joellen M; Lindström, Sara; Brennan, Paul; Bickeböller, Heike; Houlston, Richard S; Landi, Maria Teresa; Caporaso, Neil; Risch, Angela; Amin Al Olama, Ali; Berndt, Sonja I; Giovannucci, Edward L; Grönberg, Henrik; Kote-Jarai, Zsofia; Ma, Jing; Muir, Kenneth; Stampfer, Meir J; Stevens, Victoria L; Wiklund, Fredrik; Willett, Walter C; Goode, Ellen L; Permuth, Jennifer B; Risch, Harvey A; Reid, Brett M; Bezieau, Stephane; Brenner, Hermann; Chan, Andrew T; Chang-Claude, Jenny; Hudson, Thomas J; Kocarnik, Jonathan K; Newcomb, Polly A; Schoen, Robert E; Slattery, Martha L; White, Emily; Adank, Muriel A; Ahsan, Habibul; Aittomäki, Kristiina; Baglietto, Laura; Blomquist, Carl; Canzian, Federico; Czene, Kamila; Dos-Santos-Silva, Isabel; Eliassen, A Heather; Figueroa, Jonine D; Flesch-Janys, Dieter; Fletcher, Olivia; Garcia-Closas, Montserrat; Gaudet, Mia M; Johnson, Nichola; Hall, Per; Hazra, Aditi; Hein, Rebecca; Hofman, Albert; Hopper, John L; Irwanto, Astrid; Johansson, Mattias; Kaaks, Rudolf; Kibriya, Muhammad G; Lichtner, Peter; Liu, Jianjun; Lund, Eiliv; Makalic, Enes; Meindl, Alfons; Müller-Myhsok, Bertram; Muranen, Taru A; Nevanlinna, Heli; Peeters, Petra H; Peto, Julian; Prentice, Ross L; Rahman, Nazneen; Sanchez, Maria Jose; Schmidt, Daniel F; Schmutzler, Rita K; Southey, Melissa C; Tamimi, Rulla; Travis, Ruth C; Turnbull, Clare; Uitterlinden, Andre G; Wang, Zhaoming; Whittemore, Alice S; Yang, Xiaohong R; Zheng, Wei; Buchanan, Daniel D; Casey, Graham; Conti, David V; Edlund, Christopher K; Gallinger, Steven; Haile, Robert W; Jenkins, Mark; Le Marchand, Loïc; Li, Li; Lindor, Noralene M; Schmit, Stephanie L; Thibodeau, Stephen N; Woods, Michael O; Rafnar, Thorunn; Gudmundsson, Julius; Stacey, Simon N; Stefansson, Kari; Sulem, Patrick; Chen, Y Ann; Tyrer, Jonathan P; Christiani, David C; Wei, Yongyue; Shen, Hongbing; Hu, Zhibin; Shu, Xiao-Ou; Shiraishi, Kouya; Takahashi, Atsushi; Bossé, Yohan; Obeidat, Ma'en; Nickle, David; Timens, Wim; Freedman, Matthew L; Li, Qiyuan; Seminara, Daniela; Chanock, Stephen J; Gong, Jian; Peters, Ulrike; Gruber, Stephen B; Amos, Christopher I; Sellers, Thomas A; Easton, Douglas F; Hunter, David J; Haiman, Christopher A; Henderson, Brian E; Hung, Rayjean J


    Identifying genetic variants with pleiotropic associations can uncover common pathways influencing multiple cancers. We took a two-stage approach to conduct genome-wide association studies for lung, ovary, breast, prostate, and colorectal cancer from the GAME-ON/GECCO Network (61,851 cases, 61,820 controls) to identify pleiotropic loci. Findings were replicated in independent association studies (55,789 cases, 330,490 controls). We identified a novel pleiotropic association at 1q22 involving breast and lung squamous cell carcinoma, with eQTL analysis showing an association with ADAM15/THBS3 gene expression in lung. We also identified a known breast cancer locus CASP8/ALS2CR12 associated with prostate cancer, a known cancer locus at CDKN2B-AS1 with different variants associated with lung adenocarcinoma and prostate cancer, and confirmed the associations of a breast BRCA2 locus with lung and serous ovarian cancer. This is the largest study to date examining pleiotropy across multiple cancer-associated loci, identifying common mechanisms of cancer development and progression. Cancer Res; 76(17); 5103-14. ©2016 AACR.

  13. Chapter 11. Community analysis-based methods

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Y.; Wu, C.H.; Andersen, G.L.; Holden, P.A.


    Microbial communities are each a composite of populations whose presence and relative abundance in water or other environmental samples are a direct manifestation of environmental conditions, including the introduction of microbe-rich fecal material and factors promoting persistence of the microbes therein. As shown by culture-independent methods, different animal-host fecal microbial communities appear distinctive, suggesting that their community profiles can be used to differentiate fecal samples and to potentially reveal the presence of host fecal material in environmental waters. Cross-comparisons of microbial communities from different hosts also reveal relative abundances of genetic groups that can be used to distinguish sources. In increasing order of their information richness, several community analysis methods hold promise for MST applications: phospholipid fatty acid (PLFA) analysis, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP), cloning/sequencing, and PhyloChip. Specific case studies involving TRFLP and PhyloChip approaches demonstrate the ability of community-based analyses of contaminated waters to confirm a diagnosis of water quality based on host-specific marker(s). The success of community-based MST for comprehensively confirming fecal sources relies extensively upon using appropriate multivariate statistical approaches. While community-based MST is still under evaluation and development as a primary diagnostic tool, results presented herein demonstrate its promise. Coupled with its inherently comprehensive ability to capture an unprecedented amount of microbiological data that is relevant to water quality, the tools for microbial community analysis are increasingly accessible, and community-based approaches have unparalleled potential for translation into rapid, perhaps real-time, monitoring platforms.

  14. A concise method for mine soils analysis

    Energy Technology Data Exchange (ETDEWEB)

    Winkler, S.; Wildeman, T.; Robinson, R.; Herron, J.


    A large number of abandoned hard rock mines exist in Colorado and other mountain west states, many on public property. Public pressure and resulting policy changes have become a driving force in the reclamation of these sites. Two of the key reclamation issues for these sites in the occurrence of acid forming materials (AFMs) in mine soils, and acid mine drainage (AMD) issuing from mine audits. An AMD treatment system design project for the Forest Queen mine in Colorado's San Juan mountains raised the need for a simple, useable method for analysis of mine land soils, both for suitability as a construction material, and to determine the AFM content and potential for acid release. The authors have developed a simple, stepwise, go - no go test for the analysis of mine soils. Samples were collected from a variety of sites in the Silverton, CO area, and subjected to three tiers of tests including: paste pH, Eh, and 10% HCl fizz test; then total digestion in HNO{sub 3}/HCl, neutralization potential, exposure to meteoric water, and toxicity content leaching procedure (TCLP). All elemental analyses were performed with an inductively-coupled plasma (ICP) spectrometer. Elimination of samples via the first two testing tiers left two remaining samples, which were subsequently subjected to column and sequential batch tests, with further elemental analysis by ICP. Based on these tests, one sample was chosen for suitability as a constructing material for the Forest Queen treatment system basins. Further simplification, and testing on two pairs of independent soil samples, has resulted in a final analytical method suitable for general use.

  15. Clinical analysis of early breast cancer%早期乳腺癌临床分析*

    Institute of Scientific and Technical Information of China (English)

    盛陈毅; 倪启超


    Objective: To improve early det ection and diagnosis of breast cancer.Methods:Retrospective clinical analysis was done of the ages of onset of breast cancer, early diagnosis, histological types and surgical methods.Results:162 cases were clinically cured with early breast cancer, and the follow-up results showed that the 1-year and the 3-year sur-vival rates were 100% and 97.5%.Conclusion: Early detection and diagnosis of breast cancer depend primarily on clini-cians who can detect≤2cm milk block, with the combination of ultrasound and mammography.%目的:提高乳腺癌早期发现、早期诊断水平。方法:回顾性临床分析乳腺癌发病年龄、早期诊断方法、病理组织类型和手术方法。结果:162例早期乳腺癌均临床治愈出院,159例患者获随访,1年、3年生存率分别为100%、97.5%。结论:乳腺癌早期发现、早期诊断主要取决于临床医师检出≤2cm的乳块,辅以彩超和钼靶联合检查。

  16. Validation of an algorithm able to differentiate small-cell lung cancer (SCLC) from non-small-cell lung cancer (NSCLC) patients by means of a tumour marker panel: analysis of the errors.


    Paone, G; De Angelis, G.; Portalone, L.; Greco, S.; Giosué, S.; Taglienti, A.; Bisetti, A; Ameglio, F


    By means of a mathematical score previously generated by discriminant analysis on 90 lung cancer patients, a new and larger group of 261 subjects [209 with non-small-cell lung cancer (NSCLC) and 52 with small-cell lung cancer (SCLC)] was analysed to confirm the ability of the method to distinguish between these two types of cancers. The score, which included the serum neuron-specific enolase (NSE) and CYFRA-21.1 levels, permitted correct classification of 93% of the patients. When the misclas...

  17. Who Benefits From Adjuvant Radiation Therapy for Gastric Cancer? A Meta-Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Ohri, Nitin, E-mail: [Department of Radiation Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York (United States); Garg, Madhur K. [Department of Radiation Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York (United States); Aparo, Santiago; Kaubisch, Andreas [Department of Medical Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York (United States); Tome, Wolfgang [Department of Radiation Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York (United States); Kennedy, Timothy J. [Department of Surgical Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York (United States); Kalnicki, Shalom; Guha, Chandan [Department of Radiation Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York (United States)


    Purpose: Large randomized trials have demonstrated significant survival benefits with the use of adjuvant chemotherapy or chemoradiation therapy for gastric cancer. The importance of adjuvant radiation therapy (RT) remains unclear. We performed an up-to-date meta-analysis of randomized trials testing the use of RT for resectable gastric cancer. Methods and Materials: We searched MEDLINE, EMBASE, and the Cochrane Central Register of Controlled Trials for randomized trials testing adjuvant (including neoadjuvant) RT for resectable gastric cancer. Hazard ratios describing the impact of adjuvant RT on overall survival (OS) and disease-free survival (DFS) were extracted directly from the original studies or calculated from survival curves. Pooled estimates were obtained using the inverse variance method. Subgroup analyses were performed to determine whether the efficacy of RT varies with chemotherapy use, RT timing, geographic region, type of nodal dissection performed, or lymph node status. Results: Thirteen studies met all inclusion criteria and were used for this analysis. Adjuvant RT was associated with a significant improvement in both OS (HR = 0.78, 95% CI: 0.70-0.86, P<.001) and DFS (HR = 0.71, 95% CI: 0.63-0.80, P<.001). In the 5 studies that tested adjuvant chemoradiation therapy against adjuvant chemotherapy, similar effects were seen for OS (HR = 0.83, 95% CI: 0.67-1.03, P=.087) and DFS (HR = 0.77, 95% CI: 0.91-0.65, P=.002). Available data did not reveal any subgroup of patients that does not benefit from adjuvant RT. Conclusion: In randomized trials for resectable gastric cancer, adjuvant RT provides an approximately 20% improvement in both DFS and OS. Available data do not reveal a subgroup of patients that does not benefit from adjuvant RT. Further study is required to optimize the implementation of adjuvant RT for gastric cancer with regard to patient selection and integration with systemic therapy.

  18. Generalized Analysis of a Distribution Separation Method

    Directory of Open Access Journals (Sweden)

    Peng Zhang


    Full Text Available Separating two probability distributions from a mixture model that is made up of the combinations of the two is essential to a wide range of applications. For example, in information retrieval (IR, there often exists a mixture distribution consisting of a relevance distribution that we need to estimate and an irrelevance distribution that we hope to get rid of. Recently, a distribution separation method (DSM was proposed to approximate the relevance distribution, by separating a seed irrelevance distribution from the mixture distribution. It was successfully applied to an IR task, namely pseudo-relevance feedback (PRF, where the query expansion model is often a mixture term distribution. Although initially developed in the context of IR, DSM is indeed a general mathematical formulation for probability distribution separation. Thus, it is important to further generalize its basic analysis and to explore its connections to other related methods. In this article, we first extend DSM’s theoretical analysis, which was originally based on the Pearson correlation coefficient, to entropy-related measures, including the KL-divergence (Kullback–Leibler divergence, the symmetrized KL-divergence and the JS-divergence (Jensen–Shannon divergence. Second, we investigate the distribution separation idea in a well-known method, namely the mixture model feedback (MMF approach. We prove that MMF also complies with the linear combination assumption, and then, DSM’s linear separation algorithm can largely simplify the EM algorithm in MMF. These theoretical analyses, as well as further empirical evaluation results demonstrate the advantages of our DSM approach.

  19. Associations of Breast Cancer Risk Factors With Tumor Subtypes : A Pooled Analysis From the Breast Cancer Association Consortium Studies

    NARCIS (Netherlands)

    Yang, Xiaohong R.; Chang-Claude, Jenny; Goode, Ellen L.; Couch, Fergus J.; Nevanlinna, Heli; Milne, Roger L.; Gaudet, Mia; Schmidt, Marjanka K.; Broeks, Annegien; Cox, Angela; Fasching, Peter A.; Hein, Rebecca; Spurdle, Amanda B.; Blows, Fiona; Driver, Kristy; Flesch-Janys, Dieter; Heinz, Judith; Sinn, Peter; Vrieling, Alina; Heikkinen, Tuomas; Aittomaeki, Kristiina; Heikkilae, Paeivi; Blomqvist, Carl; Lissowska, Jolanta; Peplonska, Beata; Chanock, Stephen; Figueroa, Jonine; Brinton, Louise; Hall, Per; Czene, Kamila; Humphreys, Keith; Darabi, Hatef; Liu, Jianjun; Van 't Veer, Laura J.; Van Leeuwen, Flora E.; Andrulis, Irene L.; Glendon, Gord; Knight, Julia A.; Mulligan, Anna Marie; O'Malley, Frances P.; Weerasooriya, Nayana; John, Esther M.; Beckmann, Matthias W.; Hartmann, Arndt; Weihbrecht, Sebastian B.; Wachter, David L.; Jud, Sebastian M. S.; Loehberg, Christian R.; Baglietto, Laura; English, Dallas R.; Giles, Graham G.; McLean, Catriona A.; Severi, Gianluca; Lambrechts, Diether; Vandorpe, Thijs; Weltens, Caroline; Paridaens, Robert; Smeets, Ann; Neven, Patrick; Wildiers, Hans; Wang, Xianshu; Olson, Janet E.; Cafourek, Victoria; Fredericksen, Zachary; Kosel, Matthew; Vachon, Celine; Cramp, Helen E.; Connley, Daniel; Cross, Simon S.; Balasubramanian, Sabapathy P.; Reed, Malcolm W. R.; Doerk, Thilo; Bremer, Michael; Meyer, Andreas; Karstens, Johann H.; Ay, Aysun; Park-Simon, Tjoung-Won; Hillemanns, Peter; Arias Perez, Jose Ignacio; Menendez Rodriguez, Primitiva; Zamora, Pilar; Bentez, Javier; Ko, Yon-Dschun; Fischer, Hans-Peter; Hamann, Ute; Pesch, Beate; Bruening, Thomas; Justenhoven, Christina; Brauch, Hiltrud; Eccles, Diana M.; Tapper, William J.; Gerty, Sue M.; Sawyer, Elinor J.; Tomlinson, Ian P.; Jones, Angela; Kerin, Michael; Miller, Nicola; McInerney, Niall; Anton-Culver, Hoda; Ziogas, Argyrios; Shen, Chen-Yang; Hsiung, Chia-Ni; Wu, Pei-Ei; Yang, Show-Lin; Yu, Jyh-Cherng; Chen, Shou-Tung; Hsu, Giu-Cheng; Haiman, Christopher A.; Henderson, Brian E.; Le Marchand, Loic; Kolonel, Laurence N.; Lindblom, Annika; Margolin, Sara; Jakubowska, Anna; Lubinski, Jan; Huzarski, Tomasz; Byrski, Tomasz; Gorski, Bohdan; Gronwald, Jacek; Hooning, Maartje J.; Hollestelle, Antoinette; van den Ouweland, Ans M. W.; Jager, Agnes; Kriege, Mieke; Tilanus-Linthorst, Madeleine M. A.; Collee, Margriet; Wang-Gohrke, Shan; Pylkaes, Katri; Jukkola-Vuorinen, Arja; Mononen, Kari; Grip, Mervi; Hirvikoski, Pasi; Winqvist, Robert; Mannermaa, Arto; Kosma, Veli-Matti; Kauppinen, Jaana; Kataja, Vesa; Auvinen, Paeivi; Soini, Ylermi; Sironen, Reijo; Bojesen, Stig E.; Orsted, David Dynnes; Kaur-Knudsen, Diljit; Flyger, Henrik; Nordestgaard, Borge G.; Holland, Helene; Chenevix-Trench, Georgia; Manoukian, Siranoush; Barile, Monica; Radice, Paolo; Hankinson, Susan E.; Hunter, David J.; Tamimi, Rulla; Sangrajrang, Suleeporn; Brennan, Paul; Mckay, James; Odefrey, Fabrice; Gaborieau, Valerie; Devilee, Peter; Huijts, P. E. A.; Tollenaar, R. A. E. M.; Seynaeve, C.; Dite, Gillian S.; Apicella, Carmel; Hopper, John L.; Hammet, Fleur; Tsimiklis, Helen; Smith, Letitia D.; Southey, Melissa C.; Humphreys, Manjeet K.; Easton, Douglas; Pharoah, Paul; Sherman, Mark E.; Garcia-Closas, Montserrat


    Background Previous studies have suggested that breast cancer risk factors are associated with estrogen receptor (ER) and progesterone receptor (PR) expression status of the tumors. Methods We pooled tumor marker and epidemiological risk factor data from 35 568 invasive breast cancer case patients f

  20. Risk Analysis of Prostate Cancer in PRACTICAL, a Multinational Consortium, Using 25 Known Prostate Cancer Susceptibility Loci

    DEFF Research Database (Denmark)

    Amin Al Olama, Ali; Benlloch, Sara; Antoniou, Antonis C


    BACKGROUND: Genome-wide association studies have identified multiple genetic variants associated with prostate cancer risk which explain a substantial proportion of familial relative risk. These variants can be used to stratify individuals by their risk of prostate cancer. METHODS: We genotyped 2...

  1. A meta-analysis of bevacizumab combined with chemotherapy in the treatment of ovarian cancer

    Directory of Open Access Journals (Sweden)

    T S Wang


    Full Text Available Introduction: Angiogenesis plays an important role in the biology of ovarian cancer. The clinical efficacy and side effects of bevacizumab, the vascular endothelial growth factor inhibitor, on survival and toxicity in women with this ovarian cancer, was not conclusive. We performed this systematic review and meta-analysis in order to clarify the efficacy of bevacizumab combined with chemotherapy in the treatment of ovarian cancer. Materials and Methods: We searched the electronic database of MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials and CNKI for clinical controlled trials of comparing bevacizumab combined with chemotherapy and chemotherapy alone in the treatment of ovarian cancer. The primary outcomes of eligible studies included median progression-free survival (PFS, overall survival (OS, and toxicities such as enterobrosis, hypertension, albuminuria, congestive heart failure (CHF, neutrophils, thrombosis, and bleeding. The Hazard ratio (HR and relative risk were used for the meta-analysis and were expressed with 95% confidence intervals (CIs. All the statistical analyses were carried out by  Stata 11.0 software (; Stata Corporation, College Station, TX, USA. Results: We included 5 studies with 1798 cases in the bevacizumab combined with the chemotherapy group and 1810 subjects in the chemotherapy alone group. The pooled results showed that bevacizumab + chemotherapy compared with chemotherapy alone can significant prolong the median PFS (HR, 0.64; 95% CI, 0.46-0.82; P 0.05; the toxicity analysis showed that the enterobrosis, hypertension, albuminuria, neutrophils, thrombosis, and bleeding were significantly increased in the bevacizumab + chemotherapy group compared with chemotherapy alone (Pall 0.05. Conclusion: Bevacizumab combined with chemotherapy prolonged the median PFS in patients with ovarian cancer but also increase the risk of developing enterobrosis, hypertension, albuminuria, neutrophils

  2. Cannabis Smoking and Risk of Lung Cancer - A Systematic Review and Meta-Analysis

    Directory of Open Access Journals (Sweden)

    khalid BOUTI


    Full Text Available Background: Cannabis is the illicit psychoactive substance the most consumed in the world. Little is known about the association between the use of cannabis and the risk of lung cancer.Objective:The objective of this meta-analysis is to determine whether use of cannabis is a risk factor for lung cancer.Methods: We conducted a systematic review and meta-analyses of all languages articles using relevant computerised databases. MEDLINE (online PubMed, Web of knowledge, Embase, EBSCO CINAHL, ScienceDirect, Scopus, Cochrane Library, and Directory of Open Access Journals were searched to September 2014 for cohorts and case-control studies that assessed the risk of lung cancer associated with cannabis smoking.  The literature search was performed with a combination of medical subject headings terms, "cannabis" and "lung neoplasms". Data extraction: Two investigators independently analysed and extracted results from eligible studies.Our study's registration number on PROSPERO is  CRD42014008872.Results: The search strategy identified 2476 citations. 13 studies were eligible for inclusion: 2 pooled analysis of 9 case-control studies, one case-control study and 3 cohorts.The cumulative analysis for all the studies under a fixed-effects model showed that cannabis smoking determined an increased risk of developing lung cancer in the future (relative risk 1.22, 95% confidence interval 0.999–1.5; p=0.051, with no evidence of heterogeneity across the studies (I2: 34%; p¼0.01.Conclusions: The use of cannabis with or without tobacco smoking is associated with an increased risk for lung cancer.

  3. Adjuvant therapy for locally advanced renal cell cancer: A systematic review with meta-analysis

    Directory of Open Access Journals (Sweden)

    Lima Carmen SP


    Full Text Available Abstract Background Many adjuvant trials have been undertaken in an attempt to reduce the risk of recurrence among patients who undergo surgical resection for locally advanced renal cancer. However, no clear benefit has been identified to date. This systematic review was conducted to examine the exact role of adjuvant therapy in renal cancer setting. Methods Randomized controlled trials were searched comparing adjuvant therapy (chemotherapy, vaccine, immunotherapy, biochemotherapy versus no active treatment after surgery among renal cell cancer patients. Outcomes were overall survival (OS, disease-free survival (DFS, and severe toxicities. Risk ratios (RR, hazard ratios (HR and 95% confidence intervals were calculated using a fixed-effects meta-analysis. Heterogeneity was measured by I2. Different strategies of adjuvant treatment were evaluated separately. Results Ten studies (2,609 patients were included. Adjuvant therapy provided no benefits in terms of OS (HR 1.07; 95%CI 0.89 to 1.28; P = 0.48 I2 = 0% or DFS (HR 1.03; 95%CI 0.87 to 1.21; P = 0.77 I2 = 15% when compared to no treatment. No subgroup analysis (immunotherapy, vaccines, biochemotherapy and hormone therapy had relevant results. Toxicity evaluation depicted a significantly higher frequency of serious adverse events in the adjuvant group. Conclusions This analysis provided no support for the hypothesis that the agents studied provide any clinical benefit for renal cancer patients although they increase the risk of toxic effects. Randomized trials are underway to test targeted therapies, which might open a new therapeutic frontier. Until these trials yield results, no adjuvant therapy can be recommended for patients who undergo surgical resection for renal cell cancer.

  4. Analysis Method for Quantifying Vehicle Design Goals (United States)

    Fimognari, Peter; Eskridge, Richard; Martin, Adam; Lee, Michael


    A document discusses a method for using Design Structure Matrices (DSM), coupled with high-level tools representing important life-cycle parameters, to comprehensively conceptualize a flight/ground space transportation system design by dealing with such variables as performance, up-front costs, downstream operations costs, and reliability. This approach also weighs operational approaches based on their effect on upstream design variables so that it is possible to readily, yet defensively, establish linkages between operations and these upstream variables. To avoid the large range of problems that have defeated previous methods of dealing with the complex problems of transportation design, and to cut down the inefficient use of resources, the method described in the document identifies those areas that are of sufficient promise and that provide a higher grade of analysis for those issues, as well as the linkages at issue between operations and other factors. Ultimately, the system is designed to save resources and time, and allows for the evolution of operable space transportation system technology, and design and conceptual system approach targets.

  5. Water Hammer Analysis by Characteristic Method

    Directory of Open Access Journals (Sweden)

    A. R. Lohrasbi


    Full Text Available Rapid changes in the velocity of fluid in closed conduits generate large pressure, which are transmitted through the system with the speed of sound. When the fluid medium is a liquid the pressure surges and related phenomena are described as water hammer. Water hammer is caused by normal operation of the system, such as valve opening or closure, pump starts and stoppages and by abnormal condition, such as power failure. Problem statement: Water hammer causes the additional pressure in water networks. This pressure maybe defects on pipes and connections. The likely effects of water hammer must be taken into account in the structural design of pipelines and in the design of operating procedures for pumps, valves, etc. Approach: The physical phenomena of water hammer and the mathematical model which provides the basis for design computations are described. Most water hammer analysis involves computer solution by the method of characteristics. In this study water hammer is modelled with this method and effect of valve opening and closure will be surveyed with a program that is used for this purpose and with a numerical example. Results: The more rapid the closure of the valve, the more rapid is the change in momentum and hence, greater is the additional pressure developed. Conclusions/Recommendations: For preventing of water hammer defects, is recommended that valves should be open or closed slowly. Also with using the method of characteristics, we can modelled all pipe networks, and see the affects of water hammer.

  6. Multi-Spacecraft Turbulence Analysis Methods (United States)

    Horbury, Tim S.; Osman, Kareem T.

    Turbulence is ubiquitous in space plasmas, from the solar wind to supernova remnants, and on scales from the electron gyroradius to interstellar separations. Turbulence is responsible for transporting energy across space and between scales and plays a key role in plasma heating, particle acceleration and thermalisation downstream of shocks. Just as with other plasma processes such as shocks or reconnection, turbulence results in complex, structured and time-varying behaviour which is hard to measure with a single spacecraft. However, turbulence is a particularly hard phenomenon to study because it is usually broadband in nature: it covers many scales simultaneously. One must therefore use techniques to extract information on multiple scales in order to quantify plasma turbulence and its effects. The Cluster orbit takes the spacecraft through turbulent regions with a range of characteristics: the solar wind, magnetosheath, cusp and magnetosphere. In each, the nature of the turbulence (strongly driven or fully evolved; dominated by kinetic effects or largely on fluid scales), as well as characteristics of the medium (thermalised or not; high or low plasma sub- or super-Alfvenic) mean that particular techniques are better suited to the analysis of Cluster data in different locations. In this chapter, we consider a range of methods and how they are best applied to these different regions. Perhaps the most studied turbulent space plasma environment is the solar wind, see Bruno and Carbone [2005]; Goldstein et al. [2005] for recent reviews. This is the case for a number of reasons: it is scientifically important for cosmic ray and solar energetic particle scattering and propagation, for example. However, perhaps the most significant motivations for studying solar wind turbulence are pragmatic: large volumes of high quality measurements are available; the stability of the solar wind on the scales of hours makes it possible to identify statistically stationary intervals to

  7. Personality and Gastric Cancer Screening Attendance: 
A Cross-Sectional Analysis from the Miyagi Cohort Study (United States)

    Arai, Shizuha; Nakaya, Naoki; Kakizaki, Masako; Ohmori-Matsuda, Kaori; Shimazu, Taichi; Kuriyama, Shinichi; Fukao, Akira; Tsuji, Ichiro


    Objective To determine the associations between personality subscales and attendance at gastric cancer screenings in Japan. Methods A total of 21,911 residents in rural Japan who completed a short form of the Eysenck Personality Questionnaire-Revised (EPQ-R) and a questionnaire on various health habits including the number of gastric cancer screenings attended were included in the primary analysis. We defined gastric cancer screening compliance as attendance at gastric cancer screening every year for the previous 5 years; all other patterns of attendance were defined as non-compliance. We defined gastric cancer screening visiting as attendance at 1 or more screenings during the previous 5 years; lack of attendance was defined as non-visiting. We used logistic regression to estimate the odds ratios (ORs) of gastric cancer screening compliance and visiting according to 4 score levels that corresponded to the 4 EPQ-R subscales (extraversion, neuroticism, psychoticism, and lie). Result Extraversion had a significant linear, positive association with both compliance and visiting (trend, P Lie had no association with either compliance or visiting. Conclusion The personality traits of extraversion, neuroticism, and psychoticism were significantly associated with gastric cancer screening attendance. A better understanding of the association between personality and attendance could lead to the establishment of effective campaigns to motivate people to attend cancer screenings. PMID:19164872

  8. Rectosigmoid findings are not associated with proximal colon cancer: Analysis of 6 196 consecutive cases undergoing total colonoscopy

    Institute of Scientific and Technical Information of China (English)

    Makoto Okamoto; Takao Kawabe; Yutaka Yamaji; Jun Kato; Tsuneo Ikenoue; Goichi Togo; Haruhiko Yoshida; Yasushi Shiratori; Masao Omata


    AIM: To review the risk of proximal colon cancer in patients undergoing colonoscopy.METHODS: We estimated the risk of advanced proximal adenomas and cancers in 6 196 consecutive patients that underwent colonoscopy (mean age 60 years, 65% males,without prior history of colorectal examination). Neoplasms were classified as diminutive adenoma (5 mm or less),small adenoma (6-9 mm), advanced adenoma (10 mm or more, with villous component or high-grade dysplasia)and cancer (invasive adenocarcinoma). The sites of neoplasms were defined as rectosigmoid (rectum and sigmoid colon) and proximal colon (from cecum to descending colon).RESULTS: The trend of the prevalence of advanced proximal adenoma was to increase with severe rectosigmoid findings, while the prevalence of proximal colon cancer did not increase with severe rectosigmoid findings. Among the 157 patients with proximal colon cancer, 74% had no neoplasm in the rectosigmoid colon. Multivariate logisticregression analysis revealed that age was the main predictor of proximal colon cancer and existence of rectosigmoid adenoma was not a predictor of proximal colon cancer.CONCLUSION: Sigmoidoscopy is inadequate for colorectal cancer screening, especially in older populations.

  9. Identifying significant genetic regulatory networks in the prostate cancer from microarray data based on transcription factor analysis and conditional independency

    Directory of Open Access Journals (Sweden)

    Yeh Cheng-Yu


    Full Text Available Abstract Background Prostate cancer is a world wide leading cancer and it is characterized by its aggressive metastasis. According to the clinical heterogeneity, prostate cancer displays different stages and grades related to the aggressive metastasis disease. Although numerous studies used microarray analysis and traditional clustering method to identify the individual genes during the disease processes, the important gene regulations remain unclear. We present a computational method for inferring genetic regulatory networks from micorarray data automatically with transcription factor analysis and conditional independence testing to explore the potential significant gene regulatory networks that are correlated with cancer, tumor grade and stage in the prostate cancer. Results To deal with missing values in microarray data, we used a K-nearest-neighbors (KNN algorithm to determine the precise expression values. We applied web services technology to wrap the bioinformatics toolkits and databases to automatically extract the promoter regions of DNA sequences and predicted the transcription factors that regulate the gene expressions. We adopt the microarray datasets consists of 62 primary tumors, 41 normal prostate tissues from Stanford Microarray Database (SMD as a target dataset to evaluate our method. The predicted results showed that the possible biomarker genes related to cancer and denoted the androgen functions and processes may be in the development of the prostate cancer and promote the cell death in cell cycle. Our predicted results showed that sub-networks of genes SREBF1, STAT6 and PBX1 are strongly related to a high extent while ETS transcription factors ELK1, JUN and EGR2 are related to a low extent. Gene SLC22A3 may explain clinically the differentiation associated with the high grade cancer compared with low grade cancer. Enhancer of Zeste Homolg 2 (EZH2 regulated by RUNX1 and STAT3 is correlated to the pathological stage

  10. Fish intake and ovarian cancer risk: a meta-analysis of 15 case-control and cohort studies.

    Directory of Open Access Journals (Sweden)

    Pei-yue Jiang

    Full Text Available BACKGROUND: Previous epidemiological studies have shown that fish consumption may modify the risk of ovarian cancer. However, these studies yielded controversial results. The present meta-analysis was undertaken to evaluate the relationship between fish intake and ovarian cancer risk. METHODS: A literature search was carried out using Pubmed, Embase, and Cochrane Library Central database for all relevant studies up to August 2013. We pooled the relative risks (RR from individual studies using fixed-effect or random-effect model, and carried out heterogeneity and publication bias analyses. RESULTS: A total of 15 (ten case-control, and five cohort studies were included in the present meta-analysis, representing data for 889,033 female subjects and 6,087 ovarian cancer cases. We found that total fish intake was not significantly associated with the risk of ovarian cancer among cohort studies (RR = 1.04 95% CI [0.89, 1.22] as well as case-control studies (RR = 0.90, 95% CI [0.73,1.12]. There was no evidence of publication bias as suggested by Begg's test (P = 0.55 and Egger's test(P = 0.29. CONCLUSIONS: The present meta-analysis showed that total fish consumption was not significantly associated with the risk of ovarian cancer. Further analysis on different fish species and food preparation methods should be conducted in future studies.

  11. Methods to improve rehabilitation of patients following breast cancer surgery: a review of systematic reviews

    Directory of Open Access Journals (Sweden)

    Loh SY


    Full Text Available Siew Yim Loh, Aisya Nadia Musa Department of Rehabilitation Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia Context: Breast cancer is the most prevalent cancer amongst women but it has the highest survival rates amongst all cancer. Rehabilitation therapy of post-treatment effects from cancer and its treatment is needed to improve functioning and quality of life. This review investigated the range of methods for improving physical, psychosocial, occupational, and social wellbeing in women with breast cancer after receiving breast cancer surgery. Method: A search for articles published in English between the years 2009 and 2014 was carried out using The Cochrane Database of Systematic Reviews, the Database of Abstracts of Reviews of Effects, PubMed, and ScienceDirect. Search terms included: ‘breast cancer’, ‘breast carcinoma’, ‘surgery’, ‘mastectomy’, ‘lumpectomy’, ‘breast conservation’, ‘axillary lymph node dissection’, ‘rehabilitation’, 'therapy’, ‘physiotherapy’, ‘occupational therapy’, ‘psychological’, ‘psychosocial’, ‘psychotherapy’, ‘exercise’, ‘physical activity’, ‘cognitive’, ‘occupational’, ‘alternative’, ‘complementary’, and ‘systematic review’. Study selection: Systematic reviews on the effectiveness of rehabilitation methods in improving post-operative physical, and psychological outcomes for breast cancer were selected. Sixteen articles met all the eligibility criteria and were included in the review. Data extraction: Included review year, study aim, total number of participants included, and results. Data synthesis: Evidence for exercise rehabilitation is predominantly in the improvement of shoulder mobility and limb strength. Inconclusive results exist for a range of rehabilitation methods (physical, psycho-education, nutritional, alternative-complementary methods for addressing the domains of psychosocial, cognitive, and

  12. Analysis of the Indicence and Survival of Female Breast Cancer Patients in Beijing Over a 20-Year Period

    Institute of Scientific and Technical Information of China (English)

    Qijun Wang; Weixing Zhu; Xiumei Xing; Chenxu Qu


    OBJECTIVE To provide evidence for breast cancer prevention and control through epidemiological analysis of the incidence, mortality and survival rate of female breast cancer patients in Beijing.METHODS The female registration data in the Beijing urban area from 1982 to 2001 were retrospectively reviewed. The incidence, mortality and survival rate of female breast cancer patients were analyzed using routine and life-table statistical methods.RESULTS During the period of 1982 to 2001, there was a trend of an average annual increase of female breast cancer incidence of 4.6% in urban Beijing, and of 4.9% in the world-population standardized incidence.The epidemiological features of urban Beijing female breast cancer showed:(1)The incidence distribution of different age groups from 25 to 80 years elevated with two peaks at ages of 45~ and 70~ years; (2)There was an elevation in each age group over the last 20 years; (3)The incidence rate at ages of 35 to 64 reached 95.3/105, causing breast cancer to become the number one cancer in females. The changes in the survival rate showed the following: the 5-year observed survival rate (OSR)increased from 62.0% in 1982~1983 to 68.7% in 1987~1988, and the relative-survival rate (RSR) increased from 66.3% to 74.2%. The 10-year OSR and RSR in 1987~1988 were 60.3% and 65.1%, and at 15 years 57.5% and 61.3%, respectively. The mortality rate of breast cancer patients fluctuated from 8 to 10 per 105 population over the 20 years of study.CONCLUSION There is a trend of an annual increase in female breast cancer in Beijing. The 5-year survival is being improved gradually while the mortality remains stable. The results demonstrate that the principles of "early prevention, diagnosis and treatment" for breast cancer are effective in Beijing.

  13. Method and tool for network vulnerability analysis (United States)

    Swiler, Laura Painton; Phillips, Cynthia A.


    A computer system analysis tool and method that will allow for qualitative and quantitative assessment of security attributes and vulnerabilities in systems including computer networks. The invention is based on generation of attack graphs wherein each node represents a possible attack state and each edge represents a change in state caused by a single action taken by an attacker or unwitting assistant. Edges are weighted using metrics such as attacker effort, likelihood of attack success, or time to succeed. Generation of an attack graph is accomplished by matching information about attack requirements (specified in "attack templates") to information about computer system configuration (contained in a configuration file that can be updated to reflect system changes occurring during the course of an attack) and assumed attacker capabilities (reflected in "attacker profiles"). High risk attack paths, which correspond to those considered suited to application of attack countermeasures given limited resources for applying countermeasures, are identified by finding "epsilon optimal paths."

  14. Novel Method for Detection of Gastric Cancer by Hyperspectral Image Technique

    Directory of Open Access Journals (Sweden)

    Preetha Nair


    Full Text Available During the last few decades, many studies have been performed on the early detection of cancer.Gastric cancer causes about 8,00,00 deaths worldwide per year. The objective of the work is to develop a novel hyperspectral imaging algorithm for gastric cancer detection by the medical community, however, due to the amounts of data and the highly computational nature of the algorithms, running these complex algorithms can result computationally intensive. This paper, for the early detection of gastric cancer, proposes the analysis system of an endoscopic image of the stomach, which detects the abnormal region by using the change of color in the image and by providing the surface tissue information to the detector. While advanced inflammation and cancer may be easily detected, early inflammation and cancer are difficult to detect and requires more attention to be detected. This research proposes the implementat