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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

    2009-12-01

    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. Statistical methods for site-specific analysis of cancer among the A-bomb survivors

    International Nuclear Information System (INIS)

    Statistical methods are presented for joint, or simultaneous, analysis of the risks of several types of cancer for the A-bomb survivors. Previous analyses have been made either for all cancers except leukemia together, or have been done separately by cancer type. Either of these approaches has serious limitations, and the aim of joint analysis is to overcome these, while taking advantage of the strengths of each. The primary advantage of joint analysis is that models for risks of various cancer types can have some parameters in common, and others which are type-specific. This serves to overcome difficulties due to the limited data on specific cancer types. It also provides for significant tests comparing both type-specific risks and type-specific effects of modifying factors such as sex and age. These methods are exemplified here by joint analysis of three classes of cancer considered by the BEIR-V committee: (i) respiratory, (ii) digestive, and (iii) other cancers, excluding leukemia and breast cancer. The primary aim is to illustrate the general advantages of joint analyses, but in addition some comparison is made between the results of such joint analyses and the conclusions drawn by BEIR-V committee from separate analyses. (author)

  3. Electrical Bioimpedance Analysis: A New Method in Cervical Cancer Screening

    OpenAIRE

    Lopamudra Das; Soumen Das; Jyotirmoy Chatterjee

    2015-01-01

    Cervical cancer is the second most common female cancer worldwide and a disease of concern due to its high rate of incidence of about 500,000 women annually and is responsible for about 280,000 deaths in a year. The mortality and morbidity of cervical cancer are reduced through mass screening via Pap smear, but this technique suffers from very high false negativity of around 30% to 40% and hence the sensitivity of this technique is not more than 60%. Electrical bioimpedance study employing cy...

  4. Electrical Bioimpedance Analysis: A New Method in Cervical Cancer Screening

    Directory of Open Access Journals (Sweden)

    Lopamudra Das

    2015-01-01

    Full Text Available Cervical cancer is the second most common female cancer worldwide and a disease of concern due to its high rate of incidence of about 500,000 women annually and is responsible for about 280,000 deaths in a year. The mortality and morbidity of cervical cancer are reduced through mass screening via Pap smear, but this technique suffers from very high false negativity of around 30% to 40% and hence the sensitivity of this technique is not more than 60%. Electrical bioimpedance study employing cytosensors over a frequency range offers instantaneous and quantitative means to monitor cellular events and is an upcoming technique in real time to classify cells as normal and abnormal ones. This technology is exploited for label-free detection of diseases by identifying and measuring nonbiological parameters of the cell which may carry the disease signature.

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

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    Amanda L. Peterson

    2016-09-01

    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.

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

    Science.gov (United States)

    Peterson, Amanda L; Walker, Adam K; Sloan, Erica K; Creek, Darren J

    2016-01-01

    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. PMID:27669323

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

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    Jiang Wu

    2016-01-01

    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.

  8. A method for analysis of cancer incidence in atomic bomb survivors, with application to acute leukemia

    International Nuclear Information System (INIS)

    Some statistical methodology developed for the analysis of the effect of radiation on cancer incidence is described. The methods presented make use of grouped data for estimation of and testing hypotheses about temporal aspects of the radiogenic effects on cancer incidence. The suggested approach is reviewed by its application to recent data on acute leukemia incidence in the RERF Life Span Study sample. The results of these analyses suggest that, although the temporal pattern of the radiogenic excess differs markedly by age at the time of the bomb (ATB), there is no statistically significant evidence of differences in total excess leukemia by age ATB throughout the study period. (author)

  9. Fuzzy method for pre-diagnosis of breast cancer from the Fine Needle Aspirate analysis

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    Sizilio Gláucia RMA

    2012-11-01

    Full Text Available Abstract Background Across the globe, breast cancer is one of the leading causes of death among women and, currently, Fine Needle Aspirate (FNA with visual interpretation is the easiest and fastest biopsy technique for the diagnosis of this deadly disease. Unfortunately, the ability of this method to diagnose cancer correctly when the disease is present varies greatly, from 65% to 98%. This article introduces a method to assist in the diagnosis and second opinion of breast cancer from the analysis of descriptors extracted from smears of breast mass obtained by FNA, with the use of computational intelligence resources - in this case, fuzzy logic. Methods For data acquisition of FNA, the Wisconsin Diagnostic Breast Cancer Data (WDBC, from the University of California at Irvine (UCI Machine Learning Repository, available on the internet through the UCI domain was used. The knowledge acquisition process was carried out by the extraction and analysis of numerical data of the WDBC and by interviews and discussions with medical experts. The PDM-FNA-Fuzzy was developed in four steps: 1 Fuzzification Stage; 2 Rules Base; 3 Inference Stage; and 4 Defuzzification Stage. Performance cross-validation was used in the tests, with three databases with gold pattern clinical cases randomly extracted from the WDBC. The final validation was held by medical specialists in pathology, mastology and general practice, and with gold pattern clinical cases, i.e. with known and clinically confirmed diagnosis. Results The Fuzzy Method developed provides breast cancer pre-diagnosis with 98.59% sensitivity (correct pre-diagnosis of malignancies; and 85.43% specificity (correct pre-diagnosis of benign cases. Due to the high sensitivity presented, these results are considered satisfactory, both by the opinion of medical specialists in the aforementioned areas and by comparison with other studies involving breast cancer diagnosis using FNA. Conclusions This paper presents an

  10. 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.

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

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    Manavalan Radhakrishnan

    2012-01-01

    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.

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

    International Nuclear Information System (INIS)

    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

  13. 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

    2000-12-01

    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.

  14. 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.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    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, ...

  16. Fuzzy method for pre-diagnosis of breast cancer from the Fine Needle Aspirate analysis

    OpenAIRE

    Sizilio Gláucia RMA; Leite Cicília RM; Guerreiro Ana MG; Neto Adrião D Dória

    2012-01-01

    Abstract Background Across the globe, breast cancer is one of the leading causes of death among women and, currently, Fine Needle Aspirate (FNA) with visual interpretation is the easiest and fastest biopsy technique for the diagnosis of this deadly disease. Unfortunately, the ability of this method to diagnose cancer correctly when the disease is present varies greatly, from 65% to 98%. This article introduces a method to assist in the diagnosis and second opinion of breast cancer from the an...

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

    International Nuclear Information System (INIS)

    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. (authors)

  18. 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

    2009-01-01

    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.

  19. A pooled analysis of case-control studies of thyroid cancer - I. Methods

    NARCIS (Netherlands)

    Negri, E; Ron, E; Franceschi, S; Dal Maso, L; Mark, SD; Preston-Martin, S; McTiernan, A; Kolonel, L; Kleinerman, R; Land, C; Jin, F; Wingren, G; Galanti, MR; Hallquist, A; Glattre, E; Lund, E; Levi, F; Linos, D; Braga, C; La Vecchia, C

    1999-01-01

    Objective. Because the etiology of thyroid cancer is not well described, we conducted a pooled analysis of all published case-control studies, as well as two identified unpublished studies. This paper describes the major characteristics of the 14 studies included in the analysis, as well as the stat

  20. Cancer Biomarkers from Genome-Scale DNA Methylation: Comparison of Evolutionary and Semantic Analysis Methods

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    Ioannis Valavanis

    2015-11-01

    Full Text Available DNA methylation profiling exploits microarray technologies, thus yielding a wealth of high-volume data. Here, an intelligent framework is applied, encompassing epidemiological genome-scale DNA methylation data produced from the Illumina’s Infinium Human Methylation 450K Bead Chip platform, in an effort to correlate interesting methylation patterns with cancer predisposition and, in particular, breast cancer and B-cell lymphoma. Feature selection and classification are employed in order to select, from an initial set of ~480,000 methylation measurements at CpG sites, predictive cancer epigenetic biomarkers and assess their classification power for discriminating healthy versus cancer related classes. Feature selection exploits evolutionary algorithms or a graph-theoretic methodology which makes use of the semantics information included in the Gene Ontology (GO tree. The selected features, corresponding to methylation of CpG sites, attained moderate-to-high classification accuracies when imported to a series of classifiers evaluated by resampling or blindfold validation. The semantics-driven selection revealed sets of CpG sites performing similarly with evolutionary selection in the classification tasks. However, gene enrichment and pathway analysis showed that it additionally provides more descriptive sets of GO terms and KEGG pathways regarding the cancer phenotypes studied here. Results support the expediency of this methodology regarding its application in epidemiological studies.

  1. A New Method to Diagnose Cancer Based on Image Analysis of Mass Chromatograms of Volatile Organic Compounds in Urine

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    Rozhentsov А.А.

    2014-12-01

    Full Text Available The aim of investigation was to develop a technique to diagnose early cancer based on the image analysis of mass chromatograms of volatile organic compounds in urine, and assess its efficacy. Materials and Methods. The patients were grouped by nosological types: lung cancer, esophageal cancer, gastric carcinoma, colon cancer. A control group consisted of healthy individuals. Metabolic profiles of volatile organic compounds of urine were obtained using head space solid phase microextraction coupled to gas chromatography — mass spectrometry method. Results. In accordance with the processed data of mass chromatograms of volatile organic compounds of urine for each patient and their comparison with images of control individuals, we made reference metabolic profiles of oncological diseases. The proposed technique for cancer detection is easy, non-invasive, low labor intensive and affordable. According to the assessment of the results obtained, the method sensitivity is 100%, specificity — 90.62%, type I error probability — 0%, type II error probability — 9.38%. Conclusion. The findings could be used for the further understanding of etiology and pathology of various forms of oncological diseases.

  2. Critical analysis of the images methods in detection and diagnosis in breast cancer

    International Nuclear Information System (INIS)

    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)

  3. Are the most distressing concerns of men and women with inoperable lung cancer adequately assessed? A mixed-methods analysis

    OpenAIRE

    Tishelman C, Lövgren M, Broberger E, Hamberg, K and Sprangers MAG.

    2010-01-01

    PurposeStandardized questionnaires for patient-reported outcomes are generally composed of specifiedpredetermined items, although other areas may also cause patients distress. We therefore studiedreports of what was most distressing for 343 patients with inoperable lung cancer (LC) at six timepoints during the first year postdiagnosis and how these concerns were assessed by threequality-of-life and symptom questionnaires.Patients and MethodsQualitative analysis of patients’ responses to the q...

  4. Comparing paraffined and deparaffinized breast cancer tissue samples and an analysis of Raman spectroscopy and infrared methods

    Science.gov (United States)

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

    2016-05-01

    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

  5. Prostate cancer and quality of life: analysis of response shift using triangulation between methods.

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

    2014-06-01

    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.

  6. Lung cancer gene expression database analysis incorporating prior knowledge with support vector machine-based classification method

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    Huang Desheng

    2009-07-01

    Full Text Available Abstract Background A reliable and precise classification is essential for successful diagnosis and treatment of cancer. Gene expression microarrays have provided the high-throughput platform to discover genomic biomarkers for cancer diagnosis and prognosis. Rational use of the available bioinformation can not only effectively remove or suppress noise in gene chips, but also avoid one-sided results of separate experiment. However, only some studies have been aware of the importance of prior information in cancer classification. Methods Together with the application of support vector machine as the discriminant approach, we proposed one modified method that incorporated prior knowledge into cancer classification based on gene expression data to improve accuracy. A public well-known dataset, Malignant pleural mesothelioma and lung adenocarcinoma gene expression database, was used in this study. Prior knowledge is viewed here as a means of directing the classifier using known lung adenocarcinoma related genes. The procedures were performed by software R 2.80. Results The modified method performed better after incorporating prior knowledge. Accuracy of the modified method improved from 98.86% to 100% in training set and from 98.51% to 99.06% in test set. The standard deviations of the modified method decreased from 0.26% to 0 in training set and from 3.04% to 2.10% in test set. Conclusion The method that incorporates prior knowledge into discriminant analysis could effectively improve the capacity and reduce the impact of noise. This idea may have good future not only in practice but also in methodology.

  7. Saliva collection methods for DNA biomarker analysis in oral cancer patients.

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

    2013-07-01

    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.

  8. A New Cell Block Method for Multiple Immunohistochemical Analysis of Circulating Tumor Cells in Patients with Liver Cancer

    Science.gov (United States)

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

    2016-01-01

    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

  9. Integration Analysis of Three Omics Data Using Penalized Regression Methods: An Application to Bladder Cancer.

    Science.gov (United States)

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

    2015-12-01

    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

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

    Directory of Open Access Journals (Sweden)

    Gonzalo Labarca

    2016-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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)

    2011-07-01

    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

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

    International Nuclear Information System (INIS)

    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

  14. Investigations on the use of breath gas analysis with Proton Transfer Reaction Mass Spectrometry (PTR-MS) for a non-invasive method of early lung cancer detection

    OpenAIRE

    Thekedar, Bhushan

    2013-01-01

    The analysis of volatile organic compounds (VOCs) in exhaled air is an inexpensive and non-invasive method for early detection and diagnosis of human disease. This biophysical methodology in the context of a clinical study based on whether certain lung diseases (including cancer) can be identified early using proton-transfer mass spectrometry (PTR-MS) has been tested. For different groups, such as lung cancer patients, patients with other lung diseases and healthy controls in different enviro...

  15. Pink Ribbons and Red Dresses: A Mixed Methods Content Analysis of Media Coverage of Breast Cancer and Heart Disease.

    Science.gov (United States)

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

    2016-10-01

    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. PMID:26984767

  16. Analysis of trace elements in scalp hair of healthy people, hyperplasia and breast cancer patients with XRF method

    International Nuclear Information System (INIS)

    The possibilities of using the energy dispersion X-ray fluorescence analysis (XRF) and synchrotron radiation X-ray fluorescence analysis (SRXFA) for the control of trace elements (TE) content in the hair of women with mammary hyperplasia and cancer are demonstrated. Ten hair samples were taken from 25- to 60-year-old women who have been operated for mammary cancer and from 23 patients under oncologist's observation on the occasion of hyperplastic process in the mammary gland (fibrocystous mastopathy). The results of the analyses of trace elements content in the hair of 52 practically healthy women were used as control. The results demonstrated that scalp hair of patients with oncological mammary pathology are characterized by the significant decrease of the concentration of selenium (Se) and zinc (Zn), and by the increase of chromium (Cr). The Se deficit was more pronounced in patients with cancer than in those with hyperplasia (fiducial probability p<0.05)

  17. Unproven methods in cancer treatment.

    Science.gov (United States)

    Hauser, S P

    1993-07-01

    The nature-based and nontoxic image makes application of unproven methods in oncology attractive in contrast to application of a mechanized scientific medicine. The application frequency of these treatments ranges from 10% to greater than 60%. Increasingly, the promoters try to create a scientific impression through a pseudologic cancer theory, a harmless diagnostic test, and a holistic treatment of every cancer. Of the big variety of unproven methods, which are summarized in 11 groups in this review, the following are discussed: anthroposophic and other mistletoe preparations; homeopathy; Maharishi Ayur-Veda; unproven anticancer diets; orthomolecular medicine, including ascorbic acid; and methods supposedly stimulating unspecific and specific defense mechanisms. In conclusion, physicians should beware of and have knowledge of currently used unproven cancer treatments for epidemiologic, social, economic, and scientific reasons. PMID:8364081

  18. Tools for building Breast Cancer CAD methods

    International Nuclear Information System (INIS)

    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)

  19. Cancer Genome Atlas Pan-cancer Analysis Project

    Directory of Open Access Journals (Sweden)

    Kun ZHANG

    2015-04-01

    Full Text Available Cancer can exhibit different forms depending on the site of origin, cell types, the different forms of genetic mutations which also affect cancer therapeutic effect. Although many genes have been demonstrated to change a direct result of the change in phenotype, however, many cancers lineage complex molecular mechanisms are still not fully elucidated. Therefore, The Cancer Genome Atlas (TCGA Research Network analyzed a large human tumors, in order to find the molecular changes in DNA, RNA, protein and epigenetic level, The results contain a wealth of data provides us with an opportunity for common, personality and new ideas throughout the cancer lineages form a whole description. Pan-cancer genome program first compares the 12 kinds of cancer types. Analysis of different tumor molecular changes and their functions, will tell us how effective treatment method is applied to a similar phenotype of the tumor.

  20. [Cancer Genome Atlas Pan-cancer Analysis Project].

    Science.gov (United States)

    Zhang, Kun; Wang, Hong

    2015-04-01

    Cancer can exhibit different forms depending on the site of origin, cell types, the different forms of genetic mutations which also affect cancer therapeutic effect. Although many genes have been demonstrated to change a direct result of the change in phenotype, however, many cancers lineage complex molecular mechanisms are still not fully elucidated. Therefore, The Cancer Genome Atlas (TCGA) Research Network analyzed a large human tumors, in order to find the molecular changes in DNA, RNA, protein and epigenetic level, The results contain a wealth of data provides us with an opportunity for common, personality and new ideas throughout the cancer lineages form a whole description. Pan-cancer genome program first compares the 12 kinds of cancer types. Analysis of different tumor molecular changes and their functions, will tell us how effective treatment method is applied to a similar phenotype of the tumor. PMID:25936886

  1. Method development and validation for the analysis of a new anti-cancer infusion solution via HPLC.

    Science.gov (United States)

    Donnarumma, Fabrizio; Schober, Margot; Greilberger, Joachim; Matzi, Veronika; Lindenmann, Jörg; Maier, Alfred; Herwig, Ralf; Wintersteiger, Reinhold

    2011-01-01

    A fast and simple HPLC method has been developed and validated for the quantification of a completely new anti-cancer drug during the manufacturing process. The combination of four compounds including α-ketoglutaric acid, hydroxymethylfurfural, N-acetyl-L-methionine and N-acetyl-L-selenomethionine, administered intravenously, is still in test phase but has already shown promising results in cancer therapy. HPLC separation was achieved on an RP-18 column with a gradient system. However, the highly different concentrations of the compounds required a variation in the detection wavelength within one run. In order to produce a chromatogram where peaks were comparable on a similar range scale, detection at absorption maxima for the two most concentrated components was avoided. After optimization of the gradient program it was possible to detect all four substances within 14 min in spite of their strongly different chemical structure. The method developed was validated for accuracy, repeatability, reproducibility and robustness in relation to temperature and pH of buffer. Linearity as well as the limit of detection and quantification were determined. This HPLC method was found to be precise, accurate and reproducible and can be easily used for in-line process control during the manufacture of the anti-tumour infusion solution. PMID:21246718

  2. 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.

    Science.gov (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

    2016-02-01

    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

  3. 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.

    Science.gov (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

    2016-02-01

    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

  4. Pathway and network analysis of cancer genomes

    DEFF Research Database (Denmark)

    Creixell, Pau; Reimand, Jueri; Haider, Syed;

    2015-01-01

    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....

  5. Contemporary methods of treatment of colorectal cancer

    OpenAIRE

    Monika Kozłowska; Stanisław Głuszek

    2016-01-01

    Today, colorectal cancer (CRC) is the third most frequently diagnosed worldwide malignant cancer in males, and the second in females, with more than 1,200,000 new cases and more than 600,000 deaths, annually. Screening tests in oncology allow the detection of cancerous disease at an early, asymptomatic stage. The procedures most frequently performed in the case of colorectal cancer include: low anterior resection by the Dixon method (manual suture or staplers); abdominoperineal resection of t...

  6. A comparison of pathological methods of measuring lung cancer volume.

    OpenAIRE

    S. Binks; Clelland, C. A.; Layton, C

    1996-01-01

    AIM: To determine which of several pathological methods of measuring lung cancer volume compared most favourably with the gold standard. METHODS: Three pathological methods were used on 54 resected lung cancers: (1) measuring the maximum dimension and assuming a spherical shape; (2) measuring three dimensions and assuming an ellipsoidal shape; and (3) deriving the volume from the area of tumour on sequential 1 cm slices using a photocopier and an image analysis system. The gold standard was o...

  7. Breast Cancer and its Radiotherapeutic Methods

    International Nuclear Information System (INIS)

    Breast cancer is the most common cancer in women after skin cancer. In Iran, the presentation age of this cancer is younger than the global average. There are different therapeutic methods for treatment of breast cancer and the choice of treatment depends on the stage of the disease as well as its type and characteristics. Therapeutic methods include surgery, radiotherapy, and systemic therapies, each consisting of a variety of techniques. The two main surgical techniques are lumpectomy and mastectomy. The main systemic methods are biological therapy (immunotherapy), hormone therapy, and chemotherapy. Radiotherapy is mainly categorized into external-beam radiotherapy and brachytherapy. In this paper, we present a brief review of the different types of breast cancer and their treatments using conventional and modern radiotherapy methods, as well as the treatment efficacy and side effects of breast radiotherapy.

  8. Methods for Cervical Cancer Screening

    Directory of Open Access Journals (Sweden)

    Tatiana Vargas-Revilla

    2014-12-01

    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.

  9. Cancer detection by quantitative fluorescence image analysis.

    Science.gov (United States)

    Parry, W L; Hemstreet, G P

    1988-02-01

    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

  10. 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

    2011-09-01

    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.

  11. 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

    2012-02-01

    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.

  12. 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

    2011-06-03

    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.

  13. Pancreatic Cancer Imaging: Which Method?

    Directory of Open Access Journals (Sweden)

    Santo E

    2004-07-01

    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.

  14. A phase II RCT and economic analysis of three exercise delivery methods in men with prostate cancer on androgen deprivation therapy

    OpenAIRE

    Alibhai, Shabbir MH; Santa Mina, Daniel; Ritvo, Paul; Sabiston, Catherine; Krahn, Murray; Tomlinson, George; Matthew, Andrew; Segal, Roanne; Warde, Padraig; Durbano, Sara; O’Neill, Meagan; Culos-Reed, Nicole

    2015-01-01

    Background Androgen deprivation therapy is commonly used to treat prostate cancer, the most common visceral cancer in men. However, various side effects often worsen physical functioning and reduce well-being among men on this treatment. Based on existing evidence, both resistance and aerobic training provide benefits for this population yet adherence rates are often low. The method of exercise delivery (supervised in-center or home-based) may be important, yet few studies have compared diffe...

  15. Contemporary methods of treatment of colorectal cancer

    Directory of Open Access Journals (Sweden)

    Monika Kozłowska

    2016-01-01

    Full Text Available Today, colorectal cancer (CRC is the third most frequently diagnosed worldwide malignant cancer in males, and the second in females, with more than 1,200,000 new cases and more than 600,000 deaths, annually. Screening tests in oncology allow the detection of cancerous disease at an early, asymptomatic stage. The procedures most frequently performed in the case of colorectal cancer include: low anterior resection by the Dixon method (manual suture or staplers; abdominoperineal resection of the rectum by the Miles method; surgical procedure by the Hartmann method; local resection. Various techniques of preoperative radiotherapy are applied, aimed at tumour mass reduction (scheme I and/or obtaining local sterilisation (schemes I and II, which results in the reduction of local metastases (by approximately 50%, as well as an improvement with respect to long-term survival (by approximately 10%. At present, the following drugs for treatment of various forms of colorectal cancer have been registered by the Food and Drug Administration (FDA: fluorouracil capecitabine irinotecan, oxaliplatin, cetuximab, and bevacizumab. The combination of complete cytoreductive surgery (CCS, the goal of which is the removal of all visible (macroscopically cancer foci, with a simultaneous intraperitoneal chemotherapy in hyperthermia – HIPEC, destroying microscopic remains of the disease, allows the curing of some patients with peritoneal cancer. The effect of the action of monoclonal antibodies – cetuximab and panitumumab – is the inhibition of proliferation of cancer cells, intensification of their apoptosis, as well as reduction of synthesis and secretion of pro-angiogenic factors, such as interleukin 8 (IL-8 and vascular endothelial growth factor. In addition, antibodies targeted against EGFR impair the repair of DNA damage caused by chemotherapy and radiotherapy in the cells of the malignant tumour.

  16. Approaches to improve development methods for therapeutic cancer vaccines.

    Science.gov (United States)

    Ogi, Chizuru; Aruga, Atsushi

    2015-04-01

    Therapeutic cancer vaccines are an immunotherapy that amplify or induce an active immune response against tumors. Notably, limitations in the methodology for existing anti-cancer drugs may subsist while applying them to cancer vaccine therapy. A retrospective analysis was performed using information obtained from ClinicalTrials.gov, PubMed, and published articles. Our research evaluated the optimal methodologies for therapeutic cancer vaccines based on (1) patient populations, (2) immune monitoring, (3) tumor response evaluation, and (4) supplementary therapies. Failure to optimize these methodologies at an early phase may impact development at later stages; thus, we have proposed some points to be considered during the early phase. Moreover, we compared our proposal with the guidance for industry issued by the US Food and Drug Administration in October 2011 entitled "Clinical Considerations for Therapeutic Cancer Vaccines". Consequently, while our research was aligned with the guidance, we hope it provides further insights in order to predict the risks and benefits and facilitate decisions for a new technology. We identified the following points for consideration: (1) include in the selection criteria the immunological stage with a prognostic value, which is as important as the tumor stage; (2) select immunological assays such as phenotype analysis of lymphocytes, based on their features and standardize assay methods; (3) utilize optimal response criteria for immunotherapy in therapeutic cancer vaccine trials; and (4) consider supplementary therapies, including immune checkpoint inhibitors, for future therapeutic cancer vaccines. PMID:25746315

  17. Methods of Multivariate Analysis

    CERN Document Server

    Rencher, Alvin C

    2012-01-01

    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

  18. 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

    2009-01-01

    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.

  19. Analysis of numerical methods

    CERN Document Server

    Isaacson, Eugene

    1994-01-01

    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.

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

    Science.gov (United States)

    Zhang, Zhihong; Zhu, Yu; Ling, Yun; Zhang, Lijuan; Wan, Hongwei

    2016-01-01

    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. PMID:27274283

  1. 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.

    2003-01-01

    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.

  2. THE DIAGNOSIS AND PREDICTION OF NON-MUSCLE INVASIVE BLADDER CANCER RECURRENCE, BY APPLYING CLINICAL METHODS AND FISH ANALYSIS (A REVIEW OF LITERATURE

    Directory of Open Access Journals (Sweden)

    A. V. Troyanov

    2014-08-01

    Full Text Available The review deals with the-state-of-the-art of diagnosis and prediction of non-muscle invasive bladder cancer (BC. It gives data on the chromosomal abnormalities identified in urothelial cancer cells according to the results of trials. The development of a procedure for FISH diagnosis of BC is noted to be warranted. An algorithm for interpreting the result of the FISH analysis is given. The use of data on chromosomal abnormalities as additional predictors of the course of non-muscle invasive BC is described. The application of the FISH technique in assessing the results of adjuvant treatment in patients with non-muscle invasive BC is also depicted. In summary, the main problems in the existing algorithms for its diagnosis and prediction, by employing the FISH technique, are indicated.

  3. THE DIAGNOSIS AND PREDICTION OF NON-MUSCLE INVASIVE BLADDER CANCER RECURRENCE, BY APPLYING CLINICAL METHODS AND FISH ANALYSIS (A REVIEW OF LITERATURE

    Directory of Open Access Journals (Sweden)

    A. V. Troyanov

    2012-01-01

    Full Text Available The review deals with the-state-of-the-art of diagnosis and prediction of non-muscle invasive bladder cancer (BC. It gives data on the chromosomal abnormalities identified in urothelial cancer cells according to the results of trials. The development of a procedure for FISH diagnosis of BC is noted to be warranted. An algorithm for interpreting the result of the FISH analysis is given. The use of data on chromosomal abnormalities as additional predictors of the course of non-muscle invasive BC is described. The application of the FISH technique in assessing the results of adjuvant treatment in patients with non-muscle invasive BC is also depicted. In summary, the main problems in the existing algorithms for its diagnosis and prediction, by employing the FISH technique, are indicated.

  4. Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues.

    Science.gov (United States)

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

    2007-01-01

    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.

  5. SURVIVAL ANALYSIS OF CANCER CASES FROM QIDONG CANCER REGISTRY

    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

    1999-01-01

    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.

  6. 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...

  7. 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

    2016-05-01

    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

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

    Directory of Open Access Journals (Sweden)

    D'Alò Daniela

    2008-11-01

    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

  9. 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

    2003-01-01

    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.

  10. Integrative analysis of cancer related signaling pathways

    Directory of Open Access Journals (Sweden)

    Thomas eKessler

    2013-06-01

    Full Text Available Identification and classification of cancer types and subtypes is a major issue in current cancer research. Whole genome expression profiling of cancer tissues is often the basis for such subtype classifications of tumors and different signatures for individual cancer types have been described. However, the search for best performing discriminatory gene expression signatures covering more than one cancer type remains a relevant topic in cancer research as such a signature would help understanding the common changes in signaling networks in these disease types. In this work, we explore the idea of a top down approach for sample stratification based on a module-based network of cancer relevant signaling pathways. For assembly of this network, we consider several of the most established cancer pathways. We evaluate our sample stratification approach using expression data of human breast and ovarian cancer signatures. We show that our approach performs equally well to previously reported methods besides providing the advantage to classify different cancer types. Furthermore, it allows to identify common changes in network module activity of those cancer samples.

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

    Science.gov (United States)

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

    2016-03-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Denz Hubert

    2009-09-01

    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

  13. Multivariate Regression Analysis of Prognostic Factors in Colorectal Cancer

    Institute of Scientific and Technical Information of China (English)

    YANGZuli; WANGJianping; WANGLei; DONGWenguang; HUANGYihua; QINJianzhang; ZHANWenhua

    2003-01-01

    Objective: To evaluate the relationship between clinicopathologic features and prognosis of col-orectal cancer after surgical treatment. Methods: The relationship between clinicopathological character-istics and prognosis of 941 patients with colorectal cancer after surgical treatment were investigated by univariate and multivariate analysis. Results: The overall 3- and 5-year survival rates of patients withcolorectal cancer after surgical treatment were 63.2% and 60.8% respectively with a median survival of 1841 days. Univariate analysis revealed that such factors as gross findings, degree of differentiation, depth of infiltration, nodal and distant metastasis and neoplastic intestinal obstruction were correlated with the survival rate. Dukes stages, gross tumor configuration, intramural spread and differentiation degree were shown to be available independent prognostic factors by multivariate analysis. Conclusion: Dukes stage,as the most important available independent prognostic factor for colorectal cancer (P<0.0005), can be used to assess the postoperative survival.

  14. Development of new therapeutic methods of lung cancer through team approach study (II)

    International Nuclear Information System (INIS)

    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 1, 2, 3A 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 chemotherapeutic agents in small cell lung cancer patients from 1997 with the phase two study form. We evaluated the results of this study

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

    DEFF Research Database (Denmark)

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

    2011-01-01

    Objective. 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. Sample. Six women with a diagnostic...... to delay in the diagnostic process. Some important contributors to diagnostic delay in gynecological cancer were found: lack of cancer suspicion, competing diseases, negative test results, inexpedient referral patterns and referrals without cancer suspicion. Conclusion. Our results point out process...

  16. A method to predict breast cancer stage using Medicare claims

    OpenAIRE

    Smith, Grace L.; Shih, Ya-Chen T.; Giordano, Sharon H.; Smith, Benjamin D.; Buchholz, Thomas A.

    2010-01-01

    Background In epidemiologic studies, cancer stage is an important predictor of outcomes. However, cancer stage is typically unavailable in medical insurance claims datasets, thus limiting the usefulness of such data for epidemiologic studies. Therefore, we sought to develop an algorithm to predict cancer stage based on covariates available from claims-based data. Methods We identified a cohort of 77,306 women age ≥ 66 years with stage I-IV breast cancer, using the Surveillence Epidemiology an...

  17. Pyrosequencing Analysis for Breast Cancer DNA Methylome.

    Science.gov (United States)

    Kuscu, Cem; Kuscu, Canan

    2016-01-01

    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.

  18. Differential network analysis in human cancer research.

    Science.gov (United States)

    Gill, Ryan; Datta, Somnath; Datta, Susmita

    2014-01-01

    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.

  19. Communication Network Analysis Methods.

    Science.gov (United States)

    Farace, Richard V.; Mabee, Timothy

    This paper reviews a variety of analytic procedures that can be applied to network data, discussing the assumptions and usefulness of each procedure when applied to the complexity of human communication. Special attention is paid to the network properties measured or implied by each procedure. Factor analysis and multidimensional scaling are among…

  20. Complementing Gender Analysis Methods.

    Science.gov (United States)

    Kumar, Anant

    2016-01-01

    The existing gender analysis frameworks start with a premise that men and women are equal and should be treated equally. These frameworks give emphasis on equal distribution of resources between men and women and believe that this will bring equality which is not always true. Despite equal distribution of resources, women tend to suffer and experience discrimination in many areas of their lives such as the power to control resources within social relationships, and the need for emotional security and reproductive rights within interpersonal relationships. These frameworks believe that patriarchy as an institution plays an important role in women's oppression, exploitation, and it is a barrier in their empowerment and rights. Thus, some think that by ensuring equal distribution of resources and empowering women economically, institutions like patriarchy can be challenged. These frameworks are based on proposed equality principle which puts men and women in competing roles. Thus, the real equality will never be achieved. Contrary to the existing gender analysis frameworks, the Complementing Gender Analysis framework proposed by the author provides a new approach toward gender analysis which not only recognizes the role of economic empowerment and equal distribution of resources but suggests to incorporate the concept and role of social capital, equity, and doing gender in gender analysis which is based on perceived equity principle, putting men and women in complementing roles that may lead to equality. In this article the author reviews the mainstream gender theories in development from the viewpoint of the complementary roles of gender. This alternative view is argued based on existing literature and an anecdote of observations made by the author. While criticizing the equality theory, the author offers equity theory in resolving the gender conflict by using the concept of social and psychological capital. PMID:25941756

  1. Complementing Gender Analysis Methods.

    Science.gov (United States)

    Kumar, Anant

    2016-01-01

    The existing gender analysis frameworks start with a premise that men and women are equal and should be treated equally. These frameworks give emphasis on equal distribution of resources between men and women and believe that this will bring equality which is not always true. Despite equal distribution of resources, women tend to suffer and experience discrimination in many areas of their lives such as the power to control resources within social relationships, and the need for emotional security and reproductive rights within interpersonal relationships. These frameworks believe that patriarchy as an institution plays an important role in women's oppression, exploitation, and it is a barrier in their empowerment and rights. Thus, some think that by ensuring equal distribution of resources and empowering women economically, institutions like patriarchy can be challenged. These frameworks are based on proposed equality principle which puts men and women in competing roles. Thus, the real equality will never be achieved. Contrary to the existing gender analysis frameworks, the Complementing Gender Analysis framework proposed by the author provides a new approach toward gender analysis which not only recognizes the role of economic empowerment and equal distribution of resources but suggests to incorporate the concept and role of social capital, equity, and doing gender in gender analysis which is based on perceived equity principle, putting men and women in complementing roles that may lead to equality. In this article the author reviews the mainstream gender theories in development from the viewpoint of the complementary roles of gender. This alternative view is argued based on existing literature and an anecdote of observations made by the author. While criticizing the equality theory, the author offers equity theory in resolving the gender conflict by using the concept of social and psychological capital.

  2. Comprehensive analysis of NuMA variation in breast cancer

    Directory of Open Access Journals (Sweden)

    Aittomäki Kristiina

    2008-03-01

    Full Text Available Abstract Background A recent genome wide case-control association study identified NuMA region on 11q13 as a candidate locus for breast cancer susceptibility. Specifically, the variant Ala794Gly was suggested to be associated with increased risk of breast cancer. Methods In order to evaluate the NuMa gene for breast cancer susceptibility, we have here screened the entire coding region and exon-intron boundaries of NuMa in 92 familial breast cancer patients and constructed haplotypes of the identified variants. Five missense variants were further screened in 341 breast cancer cases with a positive family history and 368 controls. We examined the frequency of Ala794Gly in an extensive series of familial (n = 910 and unselected (n = 884 breast cancer cases and controls (n = 906, with a high power to detect the suggested breast cancer risk. We also tested if the variant is associated with histopathologic features of breast tumors. Results Screening of NuMA resulted in identification of 11 exonic variants and 12 variants in introns or untranslated regions. Five missense variants that were further screened in breast cancer cases with a positive family history and controls, were each carried on a unique haplotype. None of the variants, or the haplotypes represented by them, was associated with breast cancer risk although due to low power in this analysis, very low risk alleles may go unrecognized. The NuMA Ala794Gly showed no difference in frequency in the unselected breast cancer case series or familial case series compared to control cases. Furthermore, Ala794Gly did not show any significant association with histopathologic characteristics of the tumors, though Ala794Gly was slightly more frequent among unselected cases with lymph node involvement. Conclusion Our results do not support the role of NuMA variants as breast cancer susceptibility alleles.

  3. Diagnosis of Lung Cancer by Fractal Analysis of Damaged DNA

    Directory of Open Access Journals (Sweden)

    Hamidreza Namazi

    2015-01-01

    Full Text Available Cancer starts when cells in a part of the body start to grow out of control. In fact cells become cancer cells because of DNA damage. A DNA walk of a genome represents how the frequency of each nucleotide of a pairing nucleotide couple changes locally. In this research in order to study the cancer genes, DNA walk plots of genomes of patients with lung cancer were generated using a program written in MATLAB language. The data so obtained was checked for fractal property by computing the fractal dimension using a program written in MATLAB. Also, the correlation of damaged DNA was studied using the Hurst exponent measure. We have found that the damaged DNA sequences are exhibiting higher degree of fractality and less correlation compared with normal DNA sequences. So we confirmed this method can be used for early detection of lung cancer. The method introduced in this research not only is useful for diagnosis of lung cancer but also can be applied for detection and growth analysis of different types of cancers.

  4. Method for detecting the presence of prostate cancer

    Science.gov (United States)

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

    2010-04-13

    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.

  5. 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: satishraomlsc@gmail.com [Division of Radiobiology and Toxicology, Manipal Life Sciences Centre, Manipal University, Manipal, Karnataka (India)

    2012-12-01

    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.

  6. 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.

  7. Hormonally induced modulation in the phosphate metabolites of breast cancer: analysis of in vivo 31P MRS signals with a modified prony method.

    Science.gov (United States)

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

    1997-08-01

    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.

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

    Science.gov (United States)

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

    2013-08-27

    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.

  9. Firm Analysis by Different Methods

    OpenAIRE

    Píbilová, Kateřina

    2012-01-01

    This Diploma Thesis deals with an analysis of the company made by selected methods. External environment of the company is analysed using PESTLE analysis and Porter’s five-factor model. The internal environment is analysed by means of Kralicek Quick test and Fundamental analysis. SWOT analysis represents opportunities and threats of the external environment with the strengths and weaknesses of the company. The proposal of betterment of the company’s economic management is designed on the basi...

  10. Meta-analysis of second cancer risk after radiotherapy among childhood cancer survivors

    International Nuclear Information System (INIS)

    Cancer risks among childhood cancer survivors following radiotherapy have not yet been well characterised in terms of radiation dose. A meta-analysis of studies on the excess relative risk per gray (ERR) of second cancer was conducted previously; unfortunately, the small number of eligible studies restricted quantitative evaluations. To solve this problem, a statistical method to calculate ERR estimates from other estimates was developed, and a meta-analysis was conducted again. The PubMed database was searched and 26 relevant studies were identified. ERR estimates were available in 15 studies, and for the other 11 studies, the regression-based model was used to calculate ERR estimates from other estimates. The overall ERR estimate was 0.40, which was much lower than that of atomic bomb survivors exposed as young children. Heterogeneity of the risk among studies was suggested, and a further study is needed to explore the heterogeneity among studies. (authors)

  11. 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.

    2011-07-01

    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)

  12. Analysis of Precision of Activation Analysis Method

    DEFF Research Database (Denmark)

    Heydorn, Kaj; Nørgaard, K.

    1973-01-01

    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...

  13. 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

    2000-12-01

    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.

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

    International Nuclear Information System (INIS)

    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

  15. Nested methylation-specific polymerase chain reaction cancer detection method

    Science.gov (United States)

    Belinsky, Steven A.; Palmisano, William A.

    2007-05-08

    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.

  16. It's all in the details: methods in breast development and cancer

    OpenAIRE

    Bentires-Alj, Mohamed; Clarke, Robert B.; Jonkers, Jos; Smalley, Matthew; Stein, Torsten

    2009-01-01

    The inaugural European Network for Breast Development and Cancer (ENBDC) meeting on 'Methods in Mammary Gland Development and Cancer' was held in Weggis, Switzerland last April. The goal was to discuss the details of techniques used to study mammary gland biology and tumourigenesis. Highlights of this meeting included the use of four-colour fluorescence for protein co-localisation in tissue microarrays, genome analysis at single cell resolution, technical issues in the isolation of normal and...

  17. A method for voltage measurements of cancerous vs non-cancerous omentum.

    Science.gov (United States)

    Wu, W; Vitharana, K; Gorgy, T; Paterson, A; Cunnea, P; Gabra, H; Fotopoulou, C; Boutelle, M G; Drakakis, E M

    2015-08-01

    This paper presents and elaborates upon the practicalities of a method which enables the recording of voltage measurements from omental tissue in patients with advanced ovarian cancer. The key components of the proposed low-cost experimental setup are a tungsten electrode, a Ag/AgCl reference electrode and an instrumentation amplifier. Intriguingly, potential difference recordings between cancerous omentum and tissue culture media and between non-cancerous omentum and media, differ for tissue samples coming from the same patient. Further studies are warranted to assess the potential prognostic value of voltage measurements in cancerous tissue. PMID:26738030

  18. 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

    2012-01-01

    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.

  19. Human papillomavirus and breast cancer in Iran: a meta- analysis

    OpenAIRE

    Haghshenas, Mohammad Reza; Mousavi, Tahoora; Moosazadeh, Mahmood; Afshari, Mahdi

    2016-01-01

    Objective(s): This study aims to investigate the relationship between human papillomavirus (HPV) and breast cancer using meta- analysis. Materials and Methods: Relevant studies were identified reviewing the national and international databases. We also increased the search sensitivity by investigating the references as well as interview with research centers and experts. Finally, quality assessment and implementation of inclusion/exclusion criteria determined the eligible articles for meta-an...

  20. 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

  1. 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

    2010-09-01

    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.

  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

    2008-01-01

    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. Increased Incidence of Early Onset Colorectal Cancer in Arizona: A Comprehensive 15-year Analysis of the Arizona Cancer Registry

    Science.gov (United States)

    Aziz, Hassan; Pandit, Viraj; DiGiovanni, Ryan M.; Ohlson, Eric; Gruessner, Angelika C.; Jandova, Jana; Nfonsam, Valentine N.

    2016-01-01

    Introduction The aim of this study was to investigate and analyze the incidence of early-onset colorectal cancer in Arizona, using the Arizona Cancer Registry. Methods We performed a retrospective analysis of patients with colorectal cancer reported in the Arizona Cancer Registry from 1995-2010. Outcome measure: incidence of CRC in patients younger than 50 years. Results 39,623 cases of colorectal cancer were reported to the Arizona Cancer Registry during a period of 15 years. Overall, there was a 17% decrease in the incidence of CRC. However, there was a 23% increase in incidence among patients in the age group 10-50. During the same time period, 15% and 41% increase in the incidence of colon and rectal cancer was observed, respectively. The most significant increase (102%) in overall CRC incidence was seen in the age group 10-29. The highest increase (110%) in incidence of colon cancer was observed in the same age group, while the most significant increase in incidence rates (225%) of rectal cancer was seen in the age group 30-34. Conclusion Although there is an overall decrease in incidence of colorectal cancer in Arizona, alarming increase in incidence of early-onset CRC was observed; mirroring the national trends.

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

    Science.gov (United States)

    Li, Junyi; Li, Yi-Xue; Li, Yuan-Yuan

    2016-01-01

    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. PMID:27597964

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

    Directory of Open Access Journals (Sweden)

    Junyi Li

    2016-01-01

    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.

  6. 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

    2007-08-01

    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.

  7. 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

    2009-01-01

    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

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

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    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.

  9. Protein expression based multimarker analysis of breast cancer samples

    Directory of Open Access Journals (Sweden)

    Rajasekaran Ayyappan K

    2011-06-01

    Full Text Available Abstract Background Tissue microarray (TMA data are commonly used to validate the prognostic accuracy of tumor markers. For example, breast cancer TMA data have led to the identification of several promising prognostic markers of survival time. Several studies have shown that TMA data can also be used to cluster patients into clinically distinct groups. Here we use breast cancer TMA data to cluster patients into distinct prognostic groups. Methods We apply weighted correlation network analysis (WGCNA to TMA data consisting of 26 putative tumor biomarkers measured on 82 breast cancer patients. Based on this analysis we identify three groups of patients with low (5.4%, moderate (22% and high (50% mortality rates, respectively. We then develop a simple threshold rule using a subset of three markers (p53, Na-KATPase-β1, and TGF β receptor II that can approximately define these mortality groups. We compare the results of this correlation network analysis with results from a standard Cox regression analysis. Results We find that the rule-based grouping variable (referred to as WGCNA* is an independent predictor of survival time. While WGCNA* is based on protein measurements (TMA data, it validated in two independent Affymetrix microarray gene expression data (which measure mRNA abundance. We find that the WGCNA patient groups differed by 35% from mortality groups defined by a more conventional stepwise Cox regression analysis approach. Conclusions We show that correlation network methods, which are primarily used to analyze the relationships between gene products, are also useful for analyzing the relationships between patients and for defining distinct patient groups based on TMA data. We identify a rule based on three tumor markers for predicting breast cancer survival outcomes.

  10. 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;

    2008-01-01

    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...

  11. Methods for detection of subtle mutations in cancer genomes

    DEFF Research Database (Denmark)

    Dahl, Christina; Ralfkiaer, Ulrik; Guldberg, Per

    2006-01-01

    With the realization that cancer is a genetic disease, detection of mutations in genomic DNA has become an important discipline in many areas of cancer research. Although the publication of the human genome sequence and the immense technological advancements have facilitated the analysis of cancer...... genomes, detection of mutations in tumor specimens may still be challenging and fraught with technical problems. In this review, we describe current technologies for detection of small DNA mutations, including mutation scanning techniques to search for unknown mutations, and diagnostic techniques...... to detect known cancer mutations. We outline the principles of the different techniques and discuss their advantages and limitations. We also discuss critical issues that must be considered before choosing methodology, including sensitivity, specificity, limit of detection, throughput and cost, quantity...

  12. Cancer Genome Atlas Pan-cancer Analysis Project

    OpenAIRE

    Zhang, Kun; Wang, Hong

    2015-01-01

    Cancer can exhibit different forms depending on the site of origin, cell types, the different forms of genetic mutations which also affect cancer therapeutic effect. Although many genes have been demonstrated to change a direct result of the change in phenotype, however, many cancers lineage complex molecular mechanisms are still not fully elucidated. Therefore, The Cancer Genome Atlas (TCGA) Research Network analyzed a large human tumors, in order to find the molecular changes in DNA, RNA, p...

  13. SWOT ANALYSIS ON SAMPLING METHOD

    Directory of Open Access Journals (Sweden)

    CHIS ANCA OANA

    2014-07-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Saba Garshasbi

    2015-10-01

    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

  15. Statistical methods for bioimpedance analysis

    Directory of Open Access Journals (Sweden)

    Christian Tronstad

    2014-04-01

    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.

  16. Assessment of Thorium Analysis Methods

    International Nuclear Information System (INIS)

    The Assessment of thorium analytical methods for mixture power fuel consisting of titrimetry, X-ray flouresence spectrometry, UV-VIS spectrometry, alpha spectrometry, emission spectrography, polarography, chromatography (HPLC) and neutron activation were carried out. It can be concluded that analytical methods which have high accuracy (deviation standard < 3%) were; titrimetry neutron activation analysis and UV-VIS spectrometry; whereas with low accuracy method (deviation standard 3-10%) were; alpha spectrometry and emission spectrography. Ore samples can be analyzed by X-ray flourescnce spectrometry, neutron activation analysis, UV-VIS spectrometry, emission spectrography, chromatography and alpha spectometry. Concentrated samples can be analyzed by X-ray flourescence spectrometry; simulation samples can be analyzed by titrimetry, polarography and UV-VIS spectrometry, and samples of thorium as minor constituent can be analyzed by neutron activation analysis and alpha spectrometry. Thorium purity (impurities element in thorium samples) can be analyzed by emission spectography. Considering interference aspects, in general analytical methods without molecule reaction are better than those involving molecule reactions (author). 19 refs., 1 tabs

  17. Method of photon spectral analysis

    Energy Technology Data Exchange (ETDEWEB)

    Gehrke, Robert J. (Idaho Falls, ID); Putnam, Marie H. (Idaho Falls, ID); Killian, E. Wayne (Idaho Falls, ID); Helmer, Richard G. (Idaho Falls, ID); Kynaston, Ronnie L. (Blackfoot, ID); Goodwin, Scott G. (Idaho Falls, ID); Johnson, Larry O. (Pocatello, ID)

    1993-01-01

    A spectroscopic method to rapidly measure the presence of plutonium in soils, filters, smears, and glass waste forms by measuring the uranium L-shell x-ray emissions associated with the decay of plutonium. In addition, the technique can simultaneously acquire spectra of samples and automatically analyze them for the amount of americium and .gamma.-ray emitting activation and fission products present. The samples are counted with a large area, thin-window, n-type germanium spectrometer which is equally efficient for the detection of low-energy x-rays (10-2000 keV), as well as high-energy .gamma. rays (>1 MeV). A 8192- or 16,384 channel analyzer is used to acquire the entire photon spectrum at one time. A dual-energy, time-tagged pulser, that is injected into the test input of the preamplifier to monitor the energy scale, and detector resolution. The L x-ray portion of each spectrum is analyzed by a linear-least-squares spectral fitting technique. The .gamma.-ray portion of each spectrum is analyzed by a standard Ge .gamma.-ray analysis program. This method can be applied to any analysis involving x- and .gamma.-ray analysis in one spectrum and is especially useful when interferences in the x-ray region can be identified from the .gamma.-ray analysis and accommodated during the x-ray analysis.

  18. Method of photon spectral analysis

    Energy Technology Data Exchange (ETDEWEB)

    Gehrke, R.J.; Putnam, M.H.; Killian, E.W.; Helmer, R.G.; Kynaston, R.L.; Goodwin, S.G.; Johnson, L.O.

    1993-04-27

    A spectroscopic method to rapidly measure the presence of plutonium in soils, filters, smears, and glass waste forms by measuring the uranium L-shell x-ray emissions associated with the decay of plutonium. In addition, the technique can simultaneously acquire spectra of samples and automatically analyze them for the amount of americium and [gamma]-ray emitting activation and fission products present. The samples are counted with a large area, thin-window, n-type germanium spectrometer which is equally efficient for the detection of low-energy x-rays (10-2,000 keV), as well as high-energy [gamma] rays (>1 MeV). A 8,192- or 16,384 channel analyzer is used to acquire the entire photon spectrum at one time. A dual-energy, time-tagged pulser, that is injected into the test input of the preamplifier to monitor the energy scale, and detector resolution. The L x-ray portion of each spectrum is analyzed by a linear-least-squares spectral fitting technique. The [gamma]-ray portion of each spectrum is analyzed by a standard Ge [gamma]-ray analysis program. This method can be applied to any analysis involving x- and [gamma]-ray analysis in one spectrum and is especially useful when interferences in the x-ray region can be identified from the [gamma]-ray analysis and accommodated during the x-ray analysis.

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

    OpenAIRE

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

    2010-01-01

    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...

  20. Prognostic Role of Common MicroRNA Polymorphisms in Cancers: Evidence from a Meta-Analysis

    OpenAIRE

    Xia, Lingzi; Ren, Yangwu; Fang, Xue; Yin, Zhihua; Li, Xuelian; Wu, Wei; Guan, Peng; Baosen ZHOU

    2014-01-01

    Background The morbidity and mortality of cancer increase remarkably every year. It's a heavy burden for family and society. The detection of prognostic biomarkers can help to improve the theraputic effect and prolong the lifetime of patients. microRNAs have an influential role in cancer prognosis. The results of articles discussing the relationship between microRNA polymorphisms and cancer prognosis are inconsistent. Methods We conduct a meta-analysis of 19 publications concerning the associ...

  1. Management and performance features of cancer centers in Europe: A fuzzy-set analysis

    NARCIS (Netherlands)

    Wind, Anke; Lobo, Mariana Fernandes; Dijk, van Joris; Lepage-Nefkens, Isabelle; Laranja-Pontes, Jose; Conceicao Goncalves, da Vitor; Harten, van Wim; Rocha-Goncalves, Francisco Nuno

    2016-01-01

    The specific aim of this study is to identify the performance features of cancer centers in the European Union by using a fuzzy-set qualitative comparative analysis (fsQCA). The fsQCA method represents cases (cancer centers) as a combination of explanatory and outcome conditions. This study uses dat

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

    DEFF Research Database (Denmark)

    Stranzl, Thomas

    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....... Part IV of the thesis deals with the analysis of 93 patient-donor pairs that underwent hematopoietic stem cell transplantation (HCT). HCT is a standard treatment for a variety of hematological diseases. Graft-versus-host disease is a possible complication after an HCT, where the recipient´s cells...

  3. Statistical methods for bioimpedance analysis

    OpenAIRE

    Christian Tronstad; Are Hugo Pripp

    2014-01-01

    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 a...

  4. Nonlinear programming analysis and methods

    CERN Document Server

    Avriel, Mordecai

    2003-01-01

    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

  5. Music as a method of coping with cancer: A qualitative study among cancer patients in Sweden

    OpenAIRE

    Ahmadi, Fereshteh

    2013-01-01

    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 na...

  6. Gait analysis methods in rehabilitation

    Directory of Open Access Journals (Sweden)

    Baker Richard

    2006-03-01

    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

  7. Cancer Nursing Education: Literature Review and Documentary Analysis.

    Science.gov (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…

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

    Directory of Open Access Journals (Sweden)

    He LL

    2016-03-01

    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 

  9. Segmentation and Analysis of Cancer Cells in Blood Samples

    Directory of Open Access Journals (Sweden)

    Arjun Nelikanti

    2015-10-01

    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.

  10. Risk-benefit analysis and cost-effectiveness analysis of lung cancer screening by spiral CT

    International Nuclear Information System (INIS)

    Mass screening of lung cancer has been widely performed using indirect chest X-ray method in Japan. However reduction of the mortality for lung cancer is questioned. We have proposed that recently developed spiral CT should be adopted for the screening of lung cancer, since CT has an excellent detectability for small nodule. Lung Cancer Screening CT (LSCT) has been developed by author's group using spiral CT with low dose and light weight in order to make a mobile unit. In this paper risk-benefit analysis and cost-effectiveness analysis are described for the LSCT screening of lung cancer. As a risk, radiation carcinogenesis due to exposure from LSCT are compared with gain of life-expectancy by screening and men of 40 years or more and women of 45 years or more are justified. The cost per person-year is estimated for LSCT screening which is better than that of present method, although total cost is higher. The LSCT screening could be recommended if total cost is affordable. (author)

  11. IMMUNOHISTOCHEMICAL ANALYSIS OF UROTHELIAL BLADDER CANCERS

    Directory of Open Access Journals (Sweden)

    Katarina Bevizova

    2013-01-01

    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

  12. Data Analysis Methods for Paleogenomics

    DEFF Research Database (Denmark)

    Avila Arcos, Maria del Carmen

    , thanks to the introduction of NGS and the implementation of data analysis methods specific for each project. Chapters 1 to 3 have been published in peer-reviewed journals and Chapter 4 is currently in review. Chapter 5 consists of a manuscript describing initial results of an ongoing research project...... (Danmarks Grundforskningfond) 'Centre of Excellence in GeoGenetics' grant, with additional funding provided by the Danish Council for Independent Research 'Sapere Aude' programme. The thesis comprises five chapters, all of which represent different projects that involved the analysis of massive amounts...... of sequence data, generated using next-generation sequencing (NGS) technologies, from either forensic (Chapter 1) or ancient (Chapters 2-5) materials. These chapters present projects very different in nature, reflecting the diversity of questions that have become possible to address in the ancient DNA field...

  13. Economic analysis of alternative LLW disposal methods

    International Nuclear Information System (INIS)

    The Environmental Protection Agency (EPA) has evaluated the costs and benefits of alternative disposal technologies as part of its program to develop generally applicable environmental standards for the land disposal of low-level radioactive waste (LLW). Costs, population health effects and Critical Population Group (CPG) exposures resulting from alternative waste treatment and disposal methods were evaluated both in absolute terms and also relative to a base case (current practice). Incremental costs of the standard included costs for packaging, processing, transportation, and burial of waste. Benefits are defined in terms of reductions in the general population health risk (expected fatal cancers and genetic effects) evaluated over 10,000 years. A cost-effectiveness ratio, defined as the incremental cost per avoided health effect, was calculated for each alternative standard. The cost-effectiveness analysis took into account a number of waste streams, hydrogeologic and climatic region settings, and waste treatment and disposal methods. This paper describes the alternatives considered and preliminary results of the cost-effectiveness analysis. 15 references, 7 figures, 3 tables

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    patient reflecting the patients' pathway through the course of the disease. We combined 2 process mapping tools, namely, value stream mapping and business process modeling notation. The first method identifies the flow in a process as timelines. The latter introduces a set of easily recognizable graphical...... elements. RESULTS: Detailed information concerning the cancer patients' pathway was obtained. The method visualized the complexities within the diagnostic pathway. The role of different participants (patient, general practitioner, and local hospitals) became clear by arranging activities according...

  15. Comparative proteomic analysis of differentially expressed proteins in human pancreatic cancer tissue

    Institute of Scientific and Technical Information of China (English)

    Jian-Hua Chen; Run-Zhou Ni; Ming-Bing Xiao; Ji-Guang Guo; Jia-Wei Zhou

    2009-01-01

    BACKGROUND:Pancreatic cancer is one of the most common malignant tumors. Early diagnosis of pancreatic cancer is dififcult because of the latent onset and lack of good biomarkers. This study aimed to look for and identify differentially expressed proteins in tissues of pancreatic cancer and adjacent noncancerous tissues by proteomic approaches so as to provide information about possible pancreatic cancer markers and therapeutic targets. METHODS:Proteins extracted from 3 paired adjacent noncancerous and cancerous pancreatic tissue specimens were separated by two-dimensional gel electrophoresis (2-DE). The protein spots exhibiting statistical alternations between the two groups through computerized image analysis were then identiifed by matrix-assisted laser desorption ionization time-of-lfight mass spectrometry (MALDI-TOF-MS). In addition, Western blotting and immunohistochemistry were performed to verify the expression of certain candidate proteins. RESULTS:Twelve proteins were signiifcantly upregulated and 4 were downregulated between cancerous and paired adjacent noncancerous pancreatic tissues. Several proteins (S100A11, Ig gamma-1 chain C region, GSTO1 and peroxiredoxin 4) were found for the ifrst time to be associated with pancreatic cancer. Differential expression of some identiifed proteins was further conifrmed by Western blotting analysis and/or immunohistochemical analysis.CONCLUSIONS:Comparative proteomic analysis using 2-DE and MALDI-TOF-MS is an effective method for identifying differentially expressed proteins that may be the potential diagnostic biomarkers and therapeutic targets for pancreatic cancer.

  16. CRCDA--Comprehensive resources for cancer NGS data analysis.

    Science.gov (United States)

    Thangam, Manonanthini; Gopal, Ramesh Kumar

    2015-01-01

    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: http://bioinfo.au-kbc.org.in/ngs/ngshome.html.

  17. Joint analysis of site-specific cancer risks for the atomic bomb survivors

    International Nuclear Information System (INIS)

    Statistical methods are presented for joint analysis of site-specific cancer risks for the atomic-bomb survivors. Previous analyses of these data, aside from those on leukemia, have been made either without regard to cancer type, or separately for types or classes of cancers. Clearly, analyses without regard to cancer type are less than satisfactory. The primary advantages of joint, rather than separate, analyses are that (1) models can be fitted with parameters common to cancer types, which can allow more-precise estimation of effects of interest, (2) significance tests can be used to compare type-specific risks, and (3) a clearer understanding may be obtained of risk-modification factors such as sex, age at exposure, and time since exposure. Joint analysis is straightforward, entailing primarily the incorporation of another factor for cancer type in the usual cross-tabulation of the data for analysis. The use of these methods is illustrated in an analysis of the three categories of cancer studied by the fifth Advisory Committee on the Biological Effects of Ionizing Radiation (BEIR V): digestive, respiratory, and other solid tumors. Based on this analysis, some criticism is made of the BEIR V-preferred models. Since the proposed methods are applicable to models for either relative or absolute risks, some comments on the use of explicit models for the absolute excess risk are also given. Although some of the gains from joint analysis are apparent from the results here, it will be important to use these methods with a more suitable choice of cancer classes and for cancer incidence data in which the diagnoses are more accurate. (author)

  18. Breast Cancer Risk in Rheumatoid Arthritis: An Update Meta-Analysis

    OpenAIRE

    Guo Tian; Jia-Ning Liang; Zhuo-Yun Wang; Dian Zhou

    2014-01-01

    Background. The incidence of breast cancer in RA patients remains controversial. Thus we performed a meta-analysis to investigate the impact of RA on breast cancer. Methods. Published literature was available from PubMed, Embase, and Cochrane Library. Pooled standardized incidence rate (SIR) was computed by random-effect model analysis. Results. We identified 16 separate studies in the present study, in which the number of patients ranged from 458 to 84,475. We did not find the increased canc...

  19. Detection of Somatic Mutations by High-Resolution DNA Melting (HRM) Analysis in Multiple Cancers

    OpenAIRE

    Jesus Gonzalez-Bosquet; Jacob Calcei; Wei, Jun S.; Montserrat Garcia-Closas; Sherman, Mark E.; Stephen Hewitt; Joseph Vockley; Jolanta Lissowska; Yang, Hannah P.; Javed Khan; Stephen Chanock

    2011-01-01

    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 rounde...

  20. Two cytological methods for screening for cervical cancer

    DEFF Research Database (Denmark)

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

    2008-01-01

    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...

  1. 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

    2004-01-01

    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.

  2. Insulin glargine and cancer risk in patients with diabetes: a meta-analysis.

    Directory of Open Access Journals (Sweden)

    Xulei Tang

    Full Text Available AIM: The role of insulin glargine as a risk factor for cancer is controversial in human studies. The aim of this meta-analysis was to evaluate the relationship between insulin glargine and cancer incidence. METHODS: All observational studies and randomized controlled trials evaluating the relationship of insulin glargine and cancer risk were identified in PubMed, Embase, Web of Science, Cochrane Library and the Chinese Biomedical Medical Literature Database, through March 2012. Odds ratios (ORs with corresponding 95% confidence interval (CI were calculated with a random-effects model. Confidence in the estimates of the obtained effects (quality of evidence was assessed by using the Grading of Recommendations Assessment, Development, and Evaluation approach. RESULTS: A total of 11 studies including 448,928 study subjects and 19,128 cancer patients were finally identified for the meta-analysis. Insulin glargine use was associated with a lower odds of cancer compared with non-glargine insulin use (OR 0.81, 95% CI 0.68 to 0.98, P = 0.03; very low-quality evidence. Glargine did not increase the odds of breast cancer (OR 0.99, 95% CI 0.68 to 1.46, P = 0.966; very low-quality evidence. Compared with non-glargine insulin, no significant association was found between insulin glargine and prostate cancer, pancreatic cancer and respiratory tract cancer. Insulin glargine use was associated with lower odds of other site-specific cancer. CONCLUSIONS: Results from the meta-analysis don't support the link between insulin glargine and an increased risk of cancer and the confidence in the estimates of the effects is very low. Further studies are needed to examine the relation between insulin glargine and cancer risk, especially breast cancer.

  3. Effectiveness analysis of new methods of cervical & breast cancer screen-ing for Changshu rural women%常熟市农村妇女“两癌”筛查新方法效果分析

    Institute of Scientific and Technical Information of China (English)

    薛峰; 罗英; 陈波

    2015-01-01

    目的:探讨将宫颈薄层液基细胞学检查(TCT)技术和乳腺超声用于妇女“两癌”(宫颈癌和乳腺癌)筛查的效果。方法2013~2014年为常熟市35~64岁妇女开展“两癌”筛查,宫颈癌初筛应用TCT,乳腺癌初筛应用临床查体和彩超检查,对初筛阳性者进行进一步检查,以宫颈癌检出率、宫颈癌及癌前病变检出率、乳腺癌检出率作为评估指标,并与2010~2011年采用巴氏涂片筛查宫颈癌、乳腺临床查体筛查乳腺癌的结果进行比较。结果“两癌”检查新方法实施2年,共完成宫颈癌筛查100075人,宫颈癌检出率为29.98/10万,宫颈癌及癌前病变检出率为296.78/10万;乳腺癌筛查76014人,乳腺癌检出率为90.77/10万;“两癌”检出率明显高于2010~2011年的老方法。结论将TCT技术用于宫颈癌筛查、乳腺超声用于乳腺癌筛查可以有效提高农村妇女“两癌”的早期预防、早期诊断和早期治疗,应建立一套合理有效的管理机制,从而降低妇女“两癌”发病率和死亡率。%Objective To discuss the efficacy of thinprep cytologic test (TCT) and breast ultrasound for screening cervi-cal cancer and breast cancer (“Two Cancers”) in the rural area of Changshu City. Methods The screening of "Two Cancers"was carried out for rural women aged 35-64 in Changshu City during 2013 to 2014. TCT was applied for pre-liminary screening of cervical cancer. Meanwhile, the physical examination and Color Doppler Ultrasound were used to screen the preliminary breast cancer. For those women whose preliminary screening results were positive, further exam-inations were needed. The accuracy of the positive findings was evaluated by the detection rates of cervical cancer, pre-cancerous lesion, and breast cancer. Then the rates were compared with those by the Pap test and the physical exami-nations during 2010 to 2011. Results The new screening methods of "Two Cancers" had

  4. Computational methods for global/local analysis

    Science.gov (United States)

    Ransom, Jonathan B.; Mccleary, Susan L.; Aminpour, Mohammad A.; Knight, Norman F., Jr.

    1992-01-01

    Computational methods for global/local analysis of structures which include both uncoupled and coupled methods are described. In addition, global/local analysis methodology for automatic refinement of incompatible global and local finite element models is developed. Representative structural analysis problems are presented to demonstrate the global/local analysis methods.

  5. Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps.

    Science.gov (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

    2015-01-01

    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

  6. Investigation of Common Symptoms of Cancer and Reliability Analysis

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    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.

  7. Cancer family history reporting: impact of method and psychosocial factors.

    Science.gov (United States)

    Kelly, Kimberly M; Shedlosky-Shoemaker, Randi; Porter, Kyle; Remy, Amber; DeSimone, Philip; Andrykowski, Michael A

    2007-06-01

    Family history is one the greatest risk factors for disease and one of the most important informational tools in medical genetics for the purpose of diagnosis, risk assessment, prevention and treatment. However, research is needed on the comparability of different methods of cancer family history assessment and the influence of psychosocial factors in family history reports. The purpose of this study was to determine if individuals had discrepancies between written and interview reports of cancer family history and the role of psychosocial factors in these discrepancies. Oncology patients (n=104) were administered a survey to assess psychosocial factors (i.e., information-seeking, worry, perceived risk, and health literacy) and were asked to provide family history in a written and an interview form. Randomization determined which form individuals received first. No differences in the amount of missing data or the amount of unspecified data were noted between the written and interview method. Psychosocial factors did not differentiate between those who had discrepancies in family history reports and those who did not have discrepancies in family history reports; although there was a trend for those with lower literacy and those who were blunters to be more discrepant on type of cancer diagnosis. In sum, this preliminary study indicates that written and interview methods of family history assessment for first degree relatives may be used interchangeably. The ability to use written methods will facilitate collection of basic family history information in the oncology clinic. PMID:17318453

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

    Directory of Open Access Journals (Sweden)

    Zviad Kovziridze

    2015-03-01

    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

  9. Rectal cancer surgery: volume-outcome analysis.

    LENUS (Irish Health Repository)

    Nugent, Emmeline

    2010-12-01

    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.

  10. Tumor specific glycoproteins and method for detecting tumorigenic cancers

    International Nuclear Information System (INIS)

    The detection of tumour specific glycoproteins (TSGP) in human sera often indicates the presence of a malignant tumour in a patient. The distinguishing characteristics of TSGP isolated from the blood sera of cancer patients are described in detail together with methods of TSGP isolation and purification. Details are also given of radioimmunoassay techniques capable of detecting very low levels of serum TSGP with high specificity. (U.K.)

  11. Analysis of oral cancer epidemiology in the US reveals state-specific trends: implications for oral cancer prevention

    Directory of Open Access Journals (Sweden)

    Ditmyer Marcia

    2008-03-01

    Full Text Available Abstract Background Downward trends have been observed in oral cancer incidence and mortality in the US over the past 30 years; however, these declines are not uniform within this population. Several studies have now demonstrated an increase in the incidence and mortality from oral cancers among certain demographic groups, which may have resulted from increased risks or risk behaviors. This study examines the underlying data that comprise these trends, to identify specific populations that may be at greater risk for morbidity and mortality from oral cancers. Methods Oral cancer incidence and mortality data analyzed for this study were generated using the National Cancer Institute's Surveillance, Epidemiology and End Results (SEER program. Results While oral cancer incidence and mortality rates have been declining over the past thirty years, these declines have reversed in the past five years among some demographic groups, including black females and white males. Sorting of these data by state revealed that eight states exhibited increasing rates of oral cancer deaths, Nevada, North Carolina, Iowa, Ohio, Maine, Idaho, North Dakota, and Wyoming, in stark contrast to the national downward trend. Furthermore, a detailed analysis of data from these states revealed increasing rates of oral cancer among older white males, also contrary to the overall trends observed at the national level. Conclusion These results signify that, despite the declining long-term trends in oral cancer incidence and mortality nationally, localized geographic areas exist where the incidence and mortality from oral cancers have been increasing. These areas represent sites where public health education and prevention efforts may be focused to target these specific populations in an effort to improve health outcomes and reduce disparities within these populations.

  12. Saliva analysis combining membrane protein purification with surface-enhanced Raman spectroscopy for nasopharyngeal cancer detection

    Science.gov (United States)

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

    2014-02-01

    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.

  13. Novel methods for spectral analysis

    Science.gov (United States)

    Roy, R.; Sumpter, B. G.; Pfeffer, G. A.; Gray, S. K.; Noid, D. W.

    1991-06-01

    In this review article, various techniques for obtaining estimates of parameters related to the spectrum of an underlying process are discussed. These techniques include the conventional nonparametric FFT approach and more recently developed parametric techniques such as maximum entropy, MUSIC, and ESPRIT, the latter two being classified as signal-subspace or eigenvector techniques. These estimators span the spectrum of possible estimators in that extremes of a priori knowledge are assumed (nonparametric versus parametric) and extremes in the underlying model of the observed process (deterministic versus stochastic) are involved. The advantage of parametric techniques is their ability to provide very accurate estimates using data from extremely short time intervals. Several applications of these novel methods for frequency analysis of very short time data are presented. These include calculation of dispersion curves, and the density of vibrational states g(ω) for many-body systems, semiclassical transition frequencies, overtone linewidths, and resonance energies of the time-dependent Schrödinger equation for few-body problems.

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

    Directory of Open Access Journals (Sweden)

    Keshava,

    2015-09-01

    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.

  15. 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

    2016-01-01

    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.

  16. 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.

  17. Comparative survival analysis of breast cancer microarray studies identifies important prognostic genetic pathways

    Directory of Open Access Journals (Sweden)

    Liu Song

    2010-10-01

    Full Text Available Abstract Background An estimated 12% of females in the United States will develop breast cancer in their lifetime. Although, there are advances in treatment options including surgery and chemotherapy, breast cancer is still the second most lethal cancer in women. Thus, there is a clear need for better methods to predict prognosis for each breast cancer patient. With the advent of large genetic databases and the reduction in cost for the experiments, researchers are faced with choosing from a large pool of potential prognostic markers from numerous breast cancer gene expression profile studies. Methods Five microarray datasets related to breast cancer were examined using gene set analysis and the cancers were categorized into different subtypes using a scoring system based on genetic pathway activity. Results We have observed that significant genes in the individual studies show little reproducibility across the datasets. From our comparative analysis, using gene pathways with clinical variables is more reliable across studies and shows promise in assessing a patient's prognosis. Conclusions This study concludes that, in light of clinical variables, there are significant gene pathways in common across the datasets. Specifically, several pathways can further significantly stratify patients for survival. These candidate pathways should help to develop a panel of significant biomarkers for the prognosis of breast cancer patients in a clinical setting.

  18. Methods for the study of mast cells in cancer.

    Science.gov (United States)

    Blatner, Nichole R; Tsai, FuNien; Khazaie, Khashayarsha

    2015-01-01

    Tumor growth requires interactions of tumor cells with a receptive and inductive microenvironment. Two major populations of tumor-infiltrating cells are considered to be essential for producing such a microenvironment: (1) proinflammatory cells that nurture the tumor with growth factors and facilitate invasion and metastasis by secreting proteases and (2) immune suppressive leukocytes including T-regulatory cells (Treg) that hinder tumor-specific CD8 T-cell responses, which otherwise could potentially reject the tumor. Among the proinflammatory cells, accumulation of mast cells (MCs) in human tumors is frequently recorded and was recently linked with poor prognosis. Causative links between mast cell infiltration and tumor progression can be deduced from animal studies. There is an interesting link between mast cells and Treg. The adoptive transfer of Treg from healthy syngeneic mice to mice susceptible to colon cancer suppresses focal mastocytosis and hinders tumor progression. Furthermore, T-cell-deficient mice susceptible to colon cancer show enhanced focal mastocytosis and tumor invasion. Here, we describe methods to assess MCs in mouse models of cancer and to investigate how MCs affect tumor epithelium. Additionally, we will detail methods used to investigate how T cells influence MCs and how MCs influence T cells. PMID:25388267

  19. 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

    2011-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    K. M. Islam

    2015-01-01

    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.

  1. Recent cancer survival in Germany: an analysis of common and less common cancers.

    Science.gov (United States)

    Jansen, Lina; Castro, Felipe A; Gondos, Adam; Krilaviciute, Agne; Barnes, Benjamin; Eberle, Andrea; Emrich, Katharina; Hentschel, Stefan; Holleczek, Bernd; Katalinic, Alexander; Brenner, Hermann

    2015-06-01

    The monitoring of cancer survival by population-based cancer registries is a prerequisite to evaluate the current quality of cancer care. Our study provides 1-, 5- and 10-year relative survival as well as 5-year relative survival conditional on 1-year survival estimates and recent survival trends for Germany using data from 11 population-based cancer registries, covering around one-third of the German population. Period analysis was used to estimate relative survival for 24 common and 11 less common cancer sites for the period 2007-2010. The German and the United States survival estimates were compared using the Surveillance, Epidemiology and End Results 13 database. Trends in cancer survival in Germany between 2002-2004 and 2008-2010 were described. Five-year relative survival increased in Germany from 2002-2004 to 2008-2010 for most cancer sites. Among the 24 most common cancers, largest improvements were seen for multiple myeloma (8.0% units), non-Hodgkin lymphoma (6.2% units), prostate cancer (5.2% units) and colorectal cancer (4.6% units). In 2007-2010, the survival disadvantage in Germany compared to the United States was largest for cancers of the mouth/pharynx (-11.0% units), thyroid (-6.8% units) and prostate (-7.5% units). Although survival estimates were much lower for elderly patients in both countries, differences in age patterns were observed for some cancer sites. The reported improvements in cancer survival might reflect advances in the quality of cancer care on the population level as well as increased use of screening in Germany. The survival differences across countries and the survival disadvantage in the elderly require further investigation. PMID:25380088

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

    Directory of Open Access Journals (Sweden)

    Zejun Lu

    2014-03-01

    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

  3. Odds ratio analysis in women with endometrial cancer

    Directory of Open Access Journals (Sweden)

    Katarzyna Plagens-Rotman

    2016-03-01

    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.

  4. 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

    2009-01-01

    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.

  5. Cost trend analysis of initial cancer treatment in Taiwan.

    Directory of Open Access Journals (Sweden)

    Tsai-Yun Li

    Full Text Available BACKGROUND: Despite the high cost of initial cancer care, that is, care in the first year after diagnosis, limited information is available for specific categories of cancer-related costs, especially costs for specific services. This study purposed to identify causes of change in cancer treatment costs over time and to perform trend analyses of the percentage of cancer patients who had received a specific treatment type and the mean cost of care for patients who had received that treatment. METHODOLOGY/PRINCIPAL FINDINGS: The analysis of trends in initial treatment costs focused on cancer-related surgery, chemotherapy, radiation therapy, and treatments other than active treatments. For each cancer-specific trend, slopes were calculated for regression models with 95% confidence intervals. Analyses of patients diagnosed in 2007 showed that the National Health Insurance (NHI system paid, on average, $10,780 for initial care of a gastric cancer patient and $10,681 for initial care of a lung cancer patient, which were inflation-adjusted increases of $6,234 and $5,522, respectively, over the 1996 care costs. During the same interval, the mean NHI payment for initial care for the five specific cancers increased significantly (p<0.05. Hospitalization costs comprised the largest portion of payments for all cancers. During 1996-2007, the use of chemotherapy and radiation therapy significantly increased in all cancer types (p<0.05. In 2007, NHI payments for initial care for these five cancers exceeded $12 billion, and gastric and lung cancers accounted for the largest share. CONCLUSIONS/SIGNIFICANCE: In addition to the growing number of NHI beneficiaries with cancer, treatment costs and the percentage of patients who undergo treatment are growing. Therefore, the NHI must accurately predict the economic burden of new chemotherapy agents and radiation therapies and may need to develop programs for stratifying patients according to their potential benefit

  6. Analysis of the efficiency of cryogenic treatment for oropharyngeal cancer

    OpenAIRE

    T. D. Tabolinovskaya; I. N. Pustynskiy

    2016-01-01

    The material for the study was the medical records of 40 patients with oropharyngeal cancer who had undergone cryogenic treatment at the N.N. Blokhin Russian Cancer Research Center in the period 1975 to 2009. Analysis of the long-term results of cryogenic treatment for primary cancer, recurrences, and traditional therapy-untreated tumor showed its efficacy in 60 % of the patients. Cancer recurrence occurred in 31 (25.8 %) patients who had completed the treatment: in 25.0 % of the primary pati...

  7. Music as a method of coping with cancer: A qualitative study among cancer patients in Sweden.

    Science.gov (United States)

    Ahmadi, Fereshteh

    2013-06-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Ghazi Sharkas

    2011-04-01

    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.

  9. Constructing an Intelligent Patent Network Analysis Method

    OpenAIRE

    Wu, Chao-Chan; Yao, Ching-Bang

    2012-01-01

    Patent network analysis, an advanced method of patent analysis, is a useful tool for technology management. This method visually displays all the relationships among the patents and enables the analysts to intuitively comprehend the overview of a set of patents in the field of the technology being studied. Although patent network analysis possesses relative advantages different from traditional methods of patent analysis, it is subject to several crucial limitations. To overcome the drawbacks...

  10. Rapid coal proximate analysis by thermogravimetric method

    Energy Technology Data Exchange (ETDEWEB)

    Mao Jianxiong; Yang Dezhong; Zhao Baozhong

    1987-09-01

    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.

  11. Association between Sleep Duration and Cancer Risk: A Meta-Analysis of Prospective Cohort Studies

    OpenAIRE

    Yan Lu; Nong Tian; Jie Yin; Yuhua Shi; Zhenping Huang

    2013-01-01

    BACKGROUND: Sleep duration has been shown to play an important role in the development of cancer. However, the results have been inconsistent. A meta-analysis with prospective cohort studies was performed to clarify the association between short or long sleep duration and cancer risk. METHODS: PubMed and Embase databases were searched for eligible publications. Pooled relative risk (RR) with 95% confidence interval (CI) was calculated using random- or fixed- model. RESULTS: A total of 10 pros...

  12. Prognostic role of CD133 expression in colorectal cancer: a meta-analysis

    OpenAIRE

    Wang Ke; Xu Jianjun; Zhang Junshu; Huang Jian

    2012-01-01

    Abstract Background CD133 has been identified as a putative cancer stem cell marker in colorectal cancer (CRC). However, the clinical and prognostic significance of CD133 in CRC remains controversial. Methods Publications were identified which assessed the clinical or prognostic significance of CD133 in CRC up to October 2012. A meta-analysis was performed to clarify the association between CD133 expression and clinical outcomes. Results A total of 12 studies met the inclusion criteria, and c...

  13. Identifying Gender-Preferred Communication Styles within Online Cancer Communities: A Retrospective, Longitudinal Analysis

    OpenAIRE

    Durant, Kathleen T.; McCray, Alexa T.; Charles Safran

    2012-01-01

    BACKGROUND: The goal of this research is to determine if different gender-preferred social styles can be observed within the user interactions at an online cancer community. To achieve this goal, we identify and measure variables that pertain to each gender-specific social style. METHODS AND FINDINGS: We perform social network and statistical analysis on the communication flow of 8,388 members at six different cancer forums over eight years. Kruskal-Wallis tests were conducted to measure the ...

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

    OpenAIRE

    Zhang, Yue(Walter Burke Institute for Theoretical Physics, California Institute of Technology, Pasadena, CA, 91125, U.S.A.); Yin, Zhihua; Shen, Li; Wan, Yan; Zhou, Baosen

    2012-01-01

    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 p...

  15. Cigarette smoking and risk of ovarian cancer: a pooled analysis of 21 case-control studies

    OpenAIRE

    Faber, Mette T.; Kjær, Susanne K.; Dehlendorff, Christian; Chang-Claude, Jenny; Klaus K. Andersen; Høgdall, Estrid; Webb, Penelope M.; Jordan, Susan J; Rossing, Mary Anne; Doherty, Jennifer A; Lurie, Galina; Pamela J Thompson; Carney, Michael E; Goodman, Marc T.; Ness, Roberta B.

    2013-01-01

    Purpose The majority of previous studies have observed an increased risk of mucinous ovarian tumors associated with cigarette smoking, but the association with other histological types is unclear. In a large pooled analysis, we examined the risk of epithelial ovarian cancer associated with multiple measures of cigarette smoking with a focus on characterizing risks according to tumor behavior and histology. Methods We used data from 21 case–control studies of ovarian cancer (19,066...

  16. Pathway analysis of bladder cancer genome-wide association study identifies novel pathways involved in bladder cancer development

    Science.gov (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

    2016-01-01

    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.

  17. Spatial Analysis of Stomach Cancer Incidence in Iran.

    Science.gov (United States)

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

    2016-01-01

    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 (pstomach cancer is clustered in the northwest of the country, further epidemiological studies are needed to identify factors contributing to this concentration.

  18. Automatic diagnosis for prostate cancer using run-length matrix method

    Science.gov (United States)

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

    2009-02-01

    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.

  19. Risk of second non-breast cancer after radiotherapy for breast cancer: A systematic review and meta-analysis of 762,468 patients

    International Nuclear Information System (INIS)

    Background and purpose: Radiotherapy for breast cancer both decreases loco-regional recurrence rates and improves overall survival. However, radiotherapy has also been associated with increased second cancer risk at exposed sites. In this meta-analysis, we estimated the risk of second non-breast cancers after radiotherapy for breast cancer. Material and methods: The databases Medline/Pubmed, Cochrane, Embase and Cinahl were systematically searched, for cohort studies on second cancer after radiotherapy for breast cancer, from inception to August 1st 2013. Included studies were to report the relative risk (RR) of second cancers comparing irradiated female breast cancer patients to unirradiated patients. Primary endpoints were all second non-breast-cancers and second cancers of the lung, esophagus, thyroid and second sarcomas. RRs were pooled using random-effects meta-analysis. Results: Thirteen studies comprising 762,468 breast cancer patients were included in the meta-analysis. Five or more years after breast cancer diagnosis radiotherapy was significantly associated with an increased risk of second non-breast cancer RR 1.12 (95% confidence interval [CI] 1.06–1.19), second cancer of the lung RR 1.39 (95% CI 1.28–1.51), esophagus RR 1.53 (95% CI 1.01–2.31) and second sarcomas RR 2.53 (95% CI 1.74–3.70). The risk increased over time, and was highest 15 or more years after breast cancer diagnosis, for second lung RR 1.66 (95% CI 1.36–2.01) and second esophagus cancer RR 2.17 (95% CI 1.11–4.25). There was no significant association between radiotherapy and second thyroid cancer. Conclusions: Radiotherapy for breast cancer is significantly associated with increased risks of second non-breast cancer, overall and in organs adjacent to the previous treatment fields. Despite a relative small absolute risk, the growing number of long-time survivors after breast cancer warrants the need for normal tissue sparing radiotherapy techniques

  20. 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

    2009-06-01

    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

  1. Pathogenic Network Analysis Predicts Candidate Genes for Cervical Cancer

    Directory of Open Access Journals (Sweden)

    Yun-Xia Zhang

    2016-01-01

    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.

  2. Software Speeds Up Analysis of Breast Cancer Risk

    Science.gov (United States)

    ... page: https://medlineplus.gov/news/fullstory_161117.html 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 ...

  3. 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

  4. Evaluation methods of SWOT analysis

    OpenAIRE

    VANĚK, Michal; Mikoláš, Milan; Žváková, Kateřina

    2012-01-01

    Strategic management is an integral part of top management. By formulating the right strategy and its subsequent implementation, a managed organization can attract and retain a comparative advantage. In order to fulfil this expectation, the strategy also has to be supported with relevant findings of performed strategic analyses. The best known and probably the most common of these is a SWOT analysis. In practice, however, the analysis is reduced to mere presentation of influence factors, whic...

  5. Immunohistochemical analysis of amylase isoenzymes in thyroid cancer.

    OpenAIRE

    Higashiyama, M; Doi, S; Tomita, N; Monden, T.; Murotani, M.; Kawasaki, Y.; Kobayashi, T.; Shimano, T; Ogawa, M; Takai, S

    1991-01-01

    The expression of amylase in various histological types of thyroid cancer was studied by an immunohistochemical technique, using a polyclonal antiamylase antiserum and two monoclonal antibodies specific for salivary and pancreatic-type amylases, respectively. Amylase was expressed in 21 of 24 (88%) thyroid cancers by polyclonal antiserum analysis. Analysis by monoclonal antibodies, however, showed that only 13 (54%) cases and three (13%) cases contained salivary-type and pancreatic-type amyla...

  6. Gene network-based cancer prognosis analysis with sparse boosting

    OpenAIRE

    Ma, Shuangge; Huang, Yuan; Huang, Jian; Fang, Kuangnan

    2012-01-01

    High-throughput gene profiling studies have been extensively conducted, searching for markers associated with cancer development and progression. In this study, we analyse cancer prognosis studies with right censored survival responses. With gene expression data, we adopt the weighted gene co-expression network analysis (WGCNA) to describe the interplay among genes. In network analysis, nodes represent genes. There are subsets of nodes, called modules, which are tightly connected to each othe...

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

    Directory of Open Access Journals (Sweden)

    Liqun Zhang

    2015-05-01

    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.

  8. 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

    2006-01-01

    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.

  9. Convergence analysis of combinations of different methods

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-12-31

    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.

  10. 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

    2013-01-01

    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.

  11. Bioinformatics analysis of breast cancer bone metastasis related geneCXCR4

    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

    2013-01-01

    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 upregulated in the tissue with breast cancer bone metastasis.Compared with the tissue without hone metastasis,there was significant difference,which indicated that CXCR4 played a vital role in breast cancer bone metastasis.Conclusions:The hioinformatics 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.

  12. 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

    2005-01-01

    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.

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

    LENUS (Irish Health Repository)

    Glynn, Ronan W

    2010-12-22

    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\\

  14. Association between Metformin Therapy and Breast Cancer Incidence and Mortality: Evidence from a Meta-Analysis

    OpenAIRE

    Yang, Ting; Yang, Yuan; Liu, Shengchun

    2015-01-01

    Purpose Metformin may be associated with a decreased risk of breast cancer. We performed a meta-analysis to assess the effect of metformin intake on breast cancer risk and mortality. Methods We performed a PubMed and EMbase search for all available studies that described the risk of breast cancer and all-cause mortality in relation to the use of metformin among patients with type 2 diabetes mellitus. Pooled relative risks (RRs) were determined using a random effects model to assess the streng...

  15. Connecting Genomic Alterations to Cancer Biology with Proteomics: The NCI Clinical Proteomic Tumor Analysis Consortium

    Energy Technology Data Exchange (ETDEWEB)

    Ellis, Matthew; Gillette, Michael; Carr, Steven A.; Paulovich, Amanda G.; Smith, Richard D.; Rodland, Karin D.; Townsend, Reid; Kinsinger, Christopher; Mesri, Mehdi; Rodriguez, Henry; Liebler, Daniel

    2013-10-03

    The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium is applying the latest generation of proteomic technologies to genomically annotated tumors from The Cancer Genome Atlas (TCGA) program, a joint initiative of the NCI and the National Human Genome Research Institute. By providing a fully integrated accounting of DNA, RNA, and protein abnormalities in individual tumors, these datasets will illuminate the complex relationship between genomic abnormalities and cancer phenotypes, thus producing biologic insights as well as a wave of novel candidate biomarkers and therapeutic targets amenable to verifi cation using targeted mass spectrometry methods.

  16. Probabilistic methods in combinatorial analysis

    CERN Document Server

    Sachkov, Vladimir N

    2014-01-01

    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

  17. Applying critical analysis - main methods

    Directory of Open Access Journals (Sweden)

    Miguel Araujo Alonso

    2012-02-01

    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.

  18. Nonlinear structural analysis using integrated force method

    Indian Academy of Sciences (India)

    N R B Krishnam Raju; J Nagabhushanam

    2000-08-01

    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.

  19. Root Cause Analysis: Methods and Mindsets.

    Science.gov (United States)

    Kluch, Jacob H.

    This instructional unit is intended for use in training operations personnel and others involved in scram analysis at nuclear power plants in the techniques of root cause analysis. Four lessons are included. The first lesson provides an overview of the goals and benefits of the root cause analysis method. Root cause analysis techniques are covered…

  20. Association between sleep duration and cancer risk: a meta-analysis of prospective cohort studies.

    Directory of Open Access Journals (Sweden)

    Yan Lu

    Full Text Available BACKGROUND: Sleep duration has been shown to play an important role in the development of cancer. However, the results have been inconsistent. A meta-analysis with prospective cohort studies was performed to clarify the association between short or long sleep duration and cancer risk. METHODS: PubMed and Embase databases were searched for eligible publications. Pooled relative risk (RR with 95% confidence interval (CI was calculated using random- or fixed- model. RESULTS: A total of 10 prospective studies (8392 incident cases and 555678 participants were included in the meta-analysis. Neither short nor long sleep duration was statistically associated with increased risk of cancer (short sleep duration: RR=1.05, 95%CI=0.90-1.24, p=0.523; long sleep duration: RR=0.92, 95%CI=0.76-1.12, p=0.415. In the subgroup by cancer type, long sleep duration was positively associated with colorectal cancer (RR=1.29, 95%CI=1.09-1.52, p=0.003. CONCLUSION: The present meta-analysis suggested that neither short nor long sleep duration was significantly associated with risk of cancer, although long sleep duration increased risk of with colorectal cancer. Large-scale well-design prospective studies are required to be conducted to further investigate the observed association.

  1. Cost Analysis: Methods and Realities.

    Science.gov (United States)

    Cummings, Martin M.

    1989-01-01

    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…

  2. Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012.

    Science.gov (United States)

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

    2015-03-01

    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).

  3. Meta-Analysis of Massage Therapy on Cancer Pain.

    Science.gov (United States)

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

    2015-07-01

    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. PMID:25784669

  4. The Spatial Distribution of Cancer Incidence in Fars Province: A GIS-Based Analysis of Cancer Registry Data

    Science.gov (United States)

    Goli, Ali; Oroei, Mahbobeh; Jalalpour, Mehdi; Faramarzi, Hossein; Askarian, Mehrdad

    2013-01-01

    Background: Cancer is a major health problem in the developing countries. Variations of its incidence rate among geographical areas are due to various contributing factors. This study was performed to assess the spatial patterns of cancer incidence in the Fars Province, based on cancer registry data and to determine geographical clusters. Methods: In this cross sectional study, the new cases of cancer were recorded from 2001 to 2009. Crude incidence rate was estimated based on age groups and sex in the counties of the Fars Province. Age-standardized incidence rates (ASR) per 100,000 was calculated in each year. Spatial autocorrelation analysis was performed in measuring the geographic patterns and clusters using geographic information system (GIS). Also, comparisons were made between ASRs in each county. Results: A total of 28,411 new cases were diagnosed with cancer during 2001-2009 in the Fars Province, 55.5% of which were men. The average age was 61.6 ± 0.5 years. The highest ASR was observed in Shiraz, which is the largest county in Fars. The Moran's Index of cancer was significantly clustered in 2004, 2005, and 2006 in total, men, and women. The type of spatial clustering was high-high cluster, that to indicate from north-west to south-east of Fars Province. Conclusions: Analysis of the spatial distribution of cancer shows significant differences from year to year and between different areas. However, a clear spatial autocorrelation is observed, which can be of great interest and importance to researchers for future epidemiological studies, and to policymakers for applying preventive measures. PMID:24319551

  5. What does cancer treatment look like in consumer cancer magazines? An exploratory analysis of photographic content in consumer cancer magazines.

    Science.gov (United States)

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

    2011-04-01

    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.

  6. 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

    International Nuclear Information System (INIS)

    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. 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. 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-type KRAS resulted in the inhibition of cell growth and

  7. Genomic analysis of epithelial ovarian cancer

    Institute of Scientific and Technical Information of China (English)

    John Farley; Laurent L Ozbun; Michael J Birrer

    2008-01-01

    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.

  8. Hybrid methods for cybersecurity analysis :

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Warren Leon,; Dunlavy, Daniel M.

    2014-01-01

    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

  9. Analysis methods for photovoltaic applications

    Energy Technology Data Exchange (ETDEWEB)

    None

    1980-01-01

    Because photovoltaic power systems are being considered for an ever-widening range of applications, it is appropriate for system designers to have knowledge of and access to photovoltaic power systems simulation models and design tools. This brochure gives brief descriptions of a variety of such aids and was compiled after surveying both manufacturers and researchers. Services available through photovoltaic module manufacturers are outlined, and computer codes for systems analysis are briefly described. (WHK)

  10. Quaternion-based discriminant analysis method for color face recognition.

    Science.gov (United States)

    Xu, Yong

    2012-01-01

    Pattern recognition techniques have been used to automatically recognize the objects, personal identities, predict the function of protein, the category of the cancer, identify lesion, perform product inspection, and so on. In this paper we propose a novel quaternion-based discriminant method. This method represents and classifies color images in a simple and mathematically tractable way. The proposed method is suitable for a large variety of real-world applications such as color face recognition and classification of the ground target shown in multispectrum remote images. This method first uses the quaternion number to denote the pixel in the color image and exploits a quaternion vector to represent the color image. This method then uses the linear discriminant analysis algorithm to transform the quaternion vector into a lower-dimensional quaternion vector and classifies it in this space. The experimental results show that the proposed method can obtain a very high accuracy for color face recognition. PMID:22937054

  11. Automated analysis of image mammogram for breast cancer diagnosis

    Science.gov (United States)

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

    2016-03-01

    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.

  12. 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...

  13. The Functional Methods of Discourse Analysis

    Institute of Scientific and Technical Information of China (English)

    覃卓敏

    2008-01-01

    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.

  14. Lung Cancer: A survival analysis using data from the National Cancer Registry Uruguay of patients diagnosed in 2008

    International Nuclear Information System (INIS)

    Full text: Objective: To analyze survival (S V)from cancer in a cohort of patients Uruguayan drawn from the population-based registry and its association with clinical predictors and welfare. Materials and Methods: Retrospective analysis of patients in which there has been diagnosis of lung cancer in 2008. From the data base incidence and mortality of the 2008 RNC observed S V is calculated and constructed Kaplan Meier curves. We compare the S V as clinical variables (sex, age, extent lesion, histological type)and health care (patients seen in mutual and services health state in Montevideo and the Interior)by log rank test. Analysis is performed multivariate (Cox regression). Excluded from analysis identified patients only by death certificate (D CO)Results: We analyzed 1077 cases. The median S V entire cohort was 293 days (approx 9 months). In univariate analysis were statistically significantly sex, age, disease extension and some histological types. There were statistically S V significantly among patients treated at public and private centers assisted in Montevideo and the inside. In multivariate analysis, significant persists association with age, disease extension and assistance in public or private centers. Conclusions: In this cohort demonstrates S V comparable lung cancer to international series and an association with clinical variables consistent with them. Statistically significant differences were observed between patients assisted in public and private, which warrants further deeper analysis to determine the cause of this difference,

  15. 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.

  16. 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.

    2015-01-01

    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

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

    Science.gov (United States)

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

    2014-12-01

    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. Willingness to pay to avoid metastatic breast cancer treatment side effects: results from a conjoint analysis

    OpenAIRE

    Lalla, Deepa; Carlton, Rashad; Santos, Eduardo; Bramley, Thomas; D’Souza, Anna

    2014-01-01

    Purpose Metastatic breast cancer (MBC) patients are treated with a variety of regimens with differing side effects that can reduce the patients’ quality of life. This study assessed the willingness to pay (WTP) to avoid side effects related to MBC treatment using conjoint analysis. Methods An online, self-administered conjoint analysis survey of US adult female MBC patients was conducted to elicit preferences for MBC treatment side effects. Attributes included in the analysis were hair loss, ...

  19. 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.

  20. Up-to-date and precise estimates of cancer patient survival: model-based period analysis.

    Science.gov (United States)

    Brenner, Hermann; Hakulinen, Timo

    2006-10-01

    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.

  1. Multi-class texture analysis in colorectal cancer histology

    Science.gov (United States)

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

    2016-06-01

    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.

  2. Earth analysis methods, subsurface feature detection methods, earth analysis devices, and articles of manufacture

    Science.gov (United States)

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

    2011-09-27

    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.

  3. Infinitesimal methods of mathematical analysis

    CERN Document Server

    Pinto, J S

    2004-01-01

    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

  4. 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)

    2011-06-15

    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.)

  5. Breast cancer screening: evidence of benefit depends on the method used

    Directory of Open Access Journals (Sweden)

    Autier Philippe

    2012-12-01

    Full Text Available Abstract In this article, we discuss the most common epidemiological methods used for evaluating the ability of mammography screening to decrease the risk of breast cancer death in general populations (effectiveness. Case-control studies usually find substantial effectiveness. However when breast cancer mortality decreases for reasons unrelated to screening, the case-control design may attribute to screening mortality reductions due to other causes. Studies based on incidence-based mortality have obtained contrasted results compatible with modest to considerable effectiveness, probably because of differences in study design and statistical analysis. In areas where screening has been widespread for a long time, the incidence of advanced breast cancer should be decreasing, which in turn would translate into reduced mortality. However, no or modest declines in the incidence of advanced breast cancer has been observed in these areas. Breast cancer mortality should decrease more rapidly in areas with early introduction of screening than in areas with late introduction of screening. Nonetheless, no difference in breast mortality trends has been observed between areas with early or late screening start. When effectiveness is assessed using incidence-based mortality studies, or the monitoring of advanced cancer incidence, or trends in mortality, the ecological bias is an inherent limitation that is not easy to control. Minimization of this bias requires data over long periods of time, careful selection of populations being compared and availability of data on major confounding factors. If case-control studies seem apparently more adequate for evaluating screening effectiveness, this design has its own limitations and results must be viewed with caution. See related Opinion article: http://www.biomedcentral.com/1741-7015/10/106 and Commentary http://www.biomedcentral.com/1741-7015/10/164

  6. Comparative proteome analysis of human epithelial ovarian cancer

    Directory of Open Access Journals (Sweden)

    Gagné Jean-Philippe

    2007-09-01

    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.

  7. Dietary intake and urinary level of cadmium and breast cancer risk: A meta-analysis.

    Science.gov (United States)

    Lin, Jinbo; Zhang, Fang; Lei, Yixiong

    2016-06-01

    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.

  8. The Qualitative Method of Impact Analysis.

    Science.gov (United States)

    Mohr, Lawrence B.

    1999-01-01

    Discusses qualitative methods of impact analysis and provides an introductory treatment of one such approach. Combines an awareness of an alternative causal epistemology with current knowledge of qualitative methods of data collection and measurement to produce an approach to the analysis of impacts. (SLD)

  9. Breast Cancer Risk in Rheumatoid Arthritis: An Update Meta-Analysis

    Directory of Open Access Journals (Sweden)

    Guo Tian

    2014-01-01

    Full Text Available Background. The incidence of breast cancer in RA patients remains controversial. Thus we performed a meta-analysis to investigate the impact of RA on breast cancer. Methods. Published literature was available from PubMed, Embase, and Cochrane Library. Pooled standardized incidence rate (SIR was computed by random-effect model analysis. Results. We identified 16 separate studies in the present study, in which the number of patients ranged from 458 to 84,475. We did not find the increased cancer risk in RA patients (SIR=0.86, 95% CI=0.72–1.02. However, subgroup analysis showed that breast cancer risk in RA patients was positively different in Caucasians (SIR=0.82, 95% CI=0.73–0.93 and non-Caucasians (SIR=1.21, 95% CI=1.19–1.23, respectively. In subgroup analysis by style, a reduced incidence was found in hospital-based case subjects (SIR=0.82, 95% CI=0.69–0.97. Similarly, subgroup analysis for adjusted factors indicated that in A3 (age and sex and A4 (age, sex, and race/ethnicity the risk was decreased (SIR=0.87, 95% CI=0.76–0.99; SIR=0.63, 95% CI=0.59–0.67. Conclusions. The meta-analysis revealed no increased breast cancer risk in RA patients. However, in the subgroup analysis, the risk of breast cancer is increased in non-Caucasians patients with RA while it decreased in Caucasian population, hospital-based case subjects, and A3 group. Such relationship may provide preference for risk of breast cancer in different population.

  10. 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

    2015-01-01

    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.

  11. Clinicopathological significance of CD133 in lung cancer: A meta-analysis.

    Science.gov (United States)

    Tan, Yaoxi; Chen, Bo; Xu, Wei; Zhao, Weihong; Wu, Jianqing

    2014-01-01

    CD133 is one of the most commonly used markers of lung cancer stem cells (CSCs), which are characterized by their ability for self-renewal and tumorigenicity. However, the clinical value and significance of CD133 in lung cancer remains controversial. Due to the limited size of the individual studies, the association between CD133 and the clinicopathological characteristics of lung cancer had not been fully elucidated. A meta-analysis based on published studies was performed with the aim of evaluating the effect of CD133 on the clinicopathological characteristics of lung cancer and to investigate the role of CSCs in the prognosis of lung cancer. A total of 15 eligible studies were included in this meta-analysis and our results indicated that a positive CD133 expression was significantly associated with poor differentiation and lymph node metastasis, although it was not associated with tumor stage or histological type. Therefore, CD133 may be considered as a prognostic maker of lung cancer. Further clinical studies, with larger patient samples, unified methods and cut-off levels to detect CD133 expression, classified by tumor stage, therapeutic schedule, follow-up time and survival events, are required to determine the role of CD133 in clinical application and the association between CD133 and the prognosis of lung cancer. PMID:24649317

  12. Physical therapy methods in the treatment and rehabilitation of cancer patients

    Science.gov (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.

    2016-08-01

    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.

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

    OpenAIRE

    Barbara Ercole; Dipen J Parekh

    2011-01-01

    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)...

  14. Diagnosis of breast cancer by tissue analysis

    Institute of Scientific and Technical Information of China (English)

    Debnath Bhattacharyya; Samir Kumar Bandyopadhyay; Tai-hoon Kim

    2013-01-01

    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.

  15. 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.

    Science.gov (United States)

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

    2016-08-10

    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.

  16. 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

    2016-08-01

    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.

  17. 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.

    Science.gov (United States)

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

    2016-01-01

    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. PMID:27517900

  18. Peculiarities of carcinomatous pleurisies in breast cancer (cytological diagnostic method

    Directory of Open Access Journals (Sweden)

    O. G. Grigoruk

    2010-01-01

    Full Text Available The specific features of carcinomatous pleurisies were studied in 119 patients with breast cancer (BC. The most characteristic properties of the structure of cells and the composition of pleural fluid were noted in infiltrating ductal and lobular BC. A differential diagnosis was made between mesothelioma (17% and ovarian cancer (25%; it was difficult to perform it in lobular cancer.

  19. Multiple regression analysis of cancer incidence around nuclear plant

    International Nuclear Information System (INIS)

    The results of a multiple regression analysis of cancer incidence in the vicinity of a nuclear plant are presented. No dependence on radiation factors (natural background, radioactive releases, total dose of all types of medical examinations) is established. At the same time a relationship between general cancer incidence, turmors of lungs, trashea, bronchi and hematopoictic tissue carcimona incidence and releases of dangerous chemical substances is revealed

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

    Institute of Scientific and Technical Information of China (English)

    XiudiSun; YaliZhang; LiandiLi; YoulinQiao

    2004-01-01

    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.

  1. Self-care Concept Analysis in Cancer Patients: An Evolutionary Concept Analysis

    Science.gov (United States)

    Hasanpour-Dehkordi, Ali

    2016-01-01

    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

  2. Probabilistic structural analysis by extremum methods

    Science.gov (United States)

    Nafday, Avinash M.

    1990-01-01

    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. 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.

  4. Pleiotropic Analysis of Lung Cancer and Blood Triglycerides.

    Science.gov (United States)

    Zuber, Verena; Marconett, Crystal N; Shi, Jianxin; Hua, Xing; Wheeler, William; Yang, Chenchen; Song, Lei; Dale, Anders M; Laplana, Marina; Risch, Angela; Witoelar, Aree; Thompson, Wesley K; Schork, Andrew J; Bettella, Francesco; Wang, Yunpeng; Djurovic, Srdjan; Zhou, Beiyun; Borok, Zea; van der Heijden, Henricus F M; de Graaf, Jacqueline; Swinkels, Dorine; Aben, Katja K; McKay, James; Hung, Rayjean J; Bikeböller, Heike; Stevens, Victoria L; Albanes, Demetrius; Caporaso, Neil E; Han, Younghun; Wei, Yongyue; Panadero, Maria Angeles; Mayordomo, Jose I; Christiani, David C; Kiemeney, Lambertus; Andreassen, Ole A; Houlston, Richard; Amos, Christopher I; Chatterjee, Nilanjan; Laird-Offringa, Ite A; Mills, Ian G; Landi, Maria Teresa

    2016-12-01

    Epidemiologically related traits may share genetic risk factors, and pleiotropic analysis could identify individual loci associated with these traits. Because of their shared epidemiological associations, we conducted pleiotropic analysis of genome-wide association studies of lung cancer (12 160 lung cancer case patients and 16 838 control subjects) and cardiovascular disease risk factors (blood lipids from 188 577 subjects, type 2 diabetes from 148 821 subjects, body mass index from 123 865 subjects, and smoking phenotypes from 74 053 subjects). We found that 6p22.1 (rs6904596, ZNF184) was associated with both lung cancer (P = 5.50x10(-6)) and blood triglycerides (P = 1.39x10(-5)). We replicated the association in 6097 lung cancer case patients and 204 657 control subjects (P = 2.40 × 10(-4)) and in 71 113 subjects with triglycerides data (P = .01). rs6904596 reached genome-wide significance in lung cancer meta-analysis (odds ratio = 1.15, 95% confidence interval = 1.10 to 1.21 ,: Pcombined = 5.20x10(-9)). The large sample size provided by the lipid GWAS data and the shared genetic risk factors between the two traits contributed to the uncovering of a hitherto unidentified genetic locus for lung cancer. PMID:27565901

  5. Comparison of supervised classification methods for protein profiling in cancer diagnosis.

    Science.gov (United States)

    Dossat, Nadège; Mangé, Alain; Solassol, Jérôme; Jacot, William; Lhermitte, Ludovic; Maudelonde, Thierry; Daurès, Jean-Pierre; Molinari, Nicolas

    2007-01-01

    A key challenge in clinical proteomics of cancer is the identification of biomarkers that could allow detection, diagnosis and prognosis of the diseases. Recent advances in mass spectrometry and proteomic instrumentations offer unique chance to rapidly identify these markers. These advances pose considerable challenges, similar to those created by microarray-based investigation, for the discovery of pattern of markers from high-dimensional data, specific to each pathologic state (e.g. normal vs cancer). We propose a three-step strategy to select important markers from high-dimensional mass spectrometry data using surface enhanced laser desorption/ionization (SELDI) technology. The first two steps are the selection of the most discriminating biomarkers with a construction of different classifiers. Finally, we compare and validate their performance and robustness using different supervised classification methods such as Support Vector Machine, Linear Discriminant Analysis, Quadratic Discriminant Analysis, Neural Networks, Classification Trees and Boosting Trees. We show that the proposed method is suitable for analysing high-throughput proteomics data and that the combination of logistic regression and Linear Discriminant Analysis outperform other methods tested. PMID:19455249

  6. Comparison of Supervised Classification Methods for Protein Profiling in Cancer Diagnosis

    Directory of Open Access Journals (Sweden)

    Nadège Dossat

    2007-01-01

    Full Text Available A key challenge in clinical proteomics of cancer is the identification of biomarkers that could allow detection, diagnosis and prognosis of the diseases. Recent advances in mass spectrometry and proteomic instrumentations offer unique chance to rapidly identify these markers. These advances pose considerable challenges, similar to those created by microarray-based investigation, for the discovery of pattern of markers from high-dimensional data, specific to each pathologic state (e.g. normal vs cancer. We propose a three-step strategy to select important markers from high-dimensional mass spectrometry data using surface enhanced laser desorption/ionization (SELDI technology. The fi rst two steps are the selection of the most discriminating biomarkers with a construction of different classifiers. Finally, we compare and validate their performance and robustness using different supervised classification methods such as Support Vector Machine, Linear Discriminant Analysis, Quadratic Discriminant Analysis, Neural Networks, Classifi cation Trees and Boosting Trees. We show that the proposed method is suitable for analysing high-throughput proteomics data and that the combination of logistic regression and Linear Discriminant Analysis outperform other methods tested.

  7. ANOVA like analysis of cancer death age

    Science.gov (United States)

    Areia, Aníbal; Mexia, João T.

    2016-06-01

    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.

  8. Computational methods in power system analysis

    CERN Document Server

    Idema, Reijer

    2014-01-01

    This book treats state-of-the-art computational methods for power flow studies and contingency analysis. In the first part the authors present the relevant computational methods and mathematical concepts. In the second part, power flow and contingency analysis are treated. Furthermore, traditional methods to solve such problems are compared to modern solvers, developed using the knowledge of the first part of the book. Finally, these solvers are analyzed both theoretically and experimentally, clearly showing the benefits of the modern approach.

  9. Studies of cancer risk among Chernobyl liquidators: materials and methods

    International Nuclear Information System (INIS)

    The current paper presents the methods and design of two case-control studies among Chernobyl liquidators - one of leukaemia and non-Hodgkin lymphoma, the other of thyroid cancer risk - carried out in Belarus, Estonia, Latvia, Lithuania and Russia. The specific objective of these studies is to estimate the radiation induced risk of these diseases among liquidators of the Chernobyl accident, and, in particular, to study the effect of exposure protraction and radiation type on the risk of radiation induced cancer in the low-to-medium- (0-500 mSv) radiation dose range. The study population consists of the approximately 10,000 Baltic, 40,000 Belarus and 51,000 Russian liquidators who worked in the 30 km zone in 1986-1987, and who were registered in the Chernobyl registry of these countries. The studies included cases diagnosed in 1993-1998 for all countries but Belarus, where the study period was extended until 2000. Four controls were selected in each country from the national cohort for each case, matched on age, gender and region of residence. Information on study subjects was obtained through face-to-face interview using a standardised questionnaire with questions on demographic factors, time, place and conditions of work as a liquidator and potential risk and confounding factors for the tumours of interest. Overall, 136 cases and 595 controls after receiving their consent were included in the studies. A method of analytical dose reconstruction has been developed, validated and applied to the estimation of doses and related uncertainties for all the subjects in the study. Dose-response analyses are underway and results are likely to have important implications to assess the adequacy of existing protection standards, which are based on risk estimates derived from analyses of the mortality of atomic bomb survivors and other high dose studies. (author)

  10. Exposure to Dichlorodiphenyltrichloroethane and the Risk of Breast Cancer: A Systematic Review and Meta-analysis

    OpenAIRE

    Park, Jae-Hong; Cha, Eun Shil; Ko, Yousun; Hwang, Myung-Sil; Hong, Jin-Hwan; Lee, Won Jin

    2014-01-01

    Objectives This study extended and updated a meta-analysis of the association between exposure to dichlorodiphenyltrichloroethane (DDT) and the risk of breast cancer. Methods We reviewed the published literature on exposure to DDE and breast cancer risk to update a meta-analysis from 2004. The total of 35 studies included 16 hospital-based case–control studies, 11 population-based case–control studies, and 10 nested case–control studies identified through keyword searches in the PubMed and EM...

  11. Integrative analysis to select cancer candidate biomarkers to targeted validation

    Science.gov (United States)

    Heberle, Henry; Domingues, Romênia R.; Granato, Daniela C.; Yokoo, Sami; Canevarolo, Rafael R.; Winck, Flavia V.; Ribeiro, Ana Carolina P.; Brandão, Thaís Bianca; Filgueiras, Paulo R.; Cruz, Karen S. P.; Barbuto, José Alexandre; Poppi, Ronei J.; Minghim, Rosane; Telles, Guilherme P.; Fonseca, Felipe Paiva; Fox, Jay W.; Santos-Silva, Alan R.; Coletta, Ricardo D.; Sherman, Nicholas E.; Paes Leme, Adriana F.

    2015-01-01

    Targeted proteomics has flourished as the method of choice for prospecting for and validating potential candidate biomarkers in many diseases. However, challenges still remain due to the lack of standardized routines that can prioritize a limited number of proteins to be further validated in human samples. To help researchers identify candidate biomarkers that best characterize their samples under study, a well-designed integrative analysis pipeline, comprising MS-based discovery, feature selection methods, clustering techniques, bioinformatic analyses and targeted approaches was performed using discovery-based proteomic data from the secretomes of three classes of human cell lines (carcinoma, melanoma and non-cancerous). Three feature selection algorithms, namely, Beta-binomial, Nearest Shrunken Centroids (NSC), and Support Vector Machine-Recursive Features Elimination (SVM-RFE), indicated a panel of 137 candidate biomarkers for carcinoma and 271 for melanoma, which were differentially abundant between the tumor classes. We further tested the strength of the pipeline in selecting candidate biomarkers by immunoblotting, human tissue microarrays, label-free targeted MS and functional experiments. In conclusion, the proposed integrative analysis was able to pre-qualify and prioritize candidate biomarkers from discovery-based proteomics to targeted MS. PMID:26540631

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

    Directory of Open Access Journals (Sweden)

    Barbara Ercole

    2011-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Q Su

    2015-01-01

    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. Dietary acrylamide and cancer risk: an updated meta-analysis.

    Science.gov (United States)

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

    2015-06-15

    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.

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

    Directory of Open Access Journals (Sweden)

    Yue ZHANG

    2012-12-01

    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.

  16. Matrix methods for bare resonator eigenvalue analysis.

    Science.gov (United States)

    Latham, W P; Dente, G C

    1980-05-15

    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.

  17. Computational structural analysis and finite element methods

    CERN Document Server

    Kaveh, A

    2014-01-01

    Graph theory gained initial prominence in science and engineering through its strong links with matrix algebra and computer science. Moreover, the structure of the mathematics is well suited to that of engineering problems in analysis and design. The methods of analysis in this book employ matrix algebra, graph theory and meta-heuristic algorithms, which are ideally suited for modern computational mechanics. Efficient methods are presented that lead to highly sparse and banded structural matrices. The main features of the book include: application of graph theory for efficient analysis; extension of the force method to finite element analysis; application of meta-heuristic algorithms to ordering and decomposition (sparse matrix technology); efficient use of symmetry and regularity in the force method; and simultaneous analysis and design of structures.

  18. Protein expression based multimarker analysis of breast cancer samples

    OpenAIRE

    Rajasekaran Ayyappan K; Maresh Erin L; Alavi Mohammad; Mah Vei; Bagryanova Lora; Yoon Nam K; Presson Angela P; Goodglick Lee; Chia David; Horvath Steve

    2011-01-01

    Abstract Background Tissue microarray (TMA) data are commonly used to validate the prognostic accuracy of tumor markers. For example, breast cancer TMA data have led to the identification of several promising prognostic markers of survival time. Several studies have shown that TMA data can also be used to cluster patients into clinically distinct groups. Here we use breast cancer TMA data to cluster patients into distinct prognostic groups. Methods We apply weighted correlation network analys...

  19. Research methods to change clinical practice for patients with rare cancers.

    Science.gov (United States)

    Billingham, Lucinda; Malottki, Kinga; Steven, Neil

    2016-02-01

    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.

  20. Little or no residual prostate cancer at radical prostatectomy: vanishing cancer or switched specimen?: a microsatellite analysis of specimen identity.

    Science.gov (United States)

    Cao, Dengfeng; Hafez, Mike; Berg, Karin; Murphy, Kathleen; Epstein, Jonathan I

    2005-04-01

    With more vigilant screening for prostate cancer, there has been an associated increase in patients with little or no residual cancer at radical prostatectomy after an initial diagnosis of minute cancer on needle biopsy. This raises a critical question as to whether the biopsy and subsequent radical prostatectomy in these patients are from the same patient. We used PCR-based microsatellite marker analysis to perform identity test in 46 men (35 with minute cancer and 11 with no residual cancer). Of them, 41 were interpretable, including 31 with minute cancer and 10 with no residual cancer. All 31 interpretable cases with minute cancer showed match between the initial biopsy and radical prostatectomy specimens. Nine of the 10 interpretable cases with no residual cancer showed match and 1 showed mismatch. The remaining 5 cases (4 with minute cancer and 1 with no residual cancer) were considered uninterpretable due to technical problems. The initial biopsy of the mismatched case had high-grade cancer (Gleason score 4 + 4 = 8) measuring 9.6 mm in length with perineural invasion. Our results confirm that, in most cases of "vanishing cancer" in radical prostatectomy specimens, it reflects a chance sampling of a minute cancer and not a switch in specimens. However, specimen switch can rarely occur, and if there is high grade or a lot of cancer on the biopsy with no or very minimal cancer in the radical prostatectomy specimen, one should evaluate for patient identity. PMID:15767799

  1. Revised assessment of cancer risk to dichloromethane II. Application of probabilistic methods to cancer risk determinations.

    OpenAIRE

    David, Raymond M.; Clewell, Harvey J.; Gentry, P. Robinan; Covington, Tammie R.; Morgott, David A.; Marino, Dale J.

    2006-01-01

    KEYWORDS - CLASSIFICATION: analysis;chemically induced;Carcinogens;Dose-Response Relationship,Drug;Environment;genetics;Glutathione;Glutathione Transferase;Humans;Inhalation Exposure;Laboratories;metabolism;methods;Markov Chains;mechanisms of carcinogenesis;Methylene Chloride;Models,Biological;Monte Carlo Method;Neoplasms;pharmacokinetics;Polymorphism,Genetic;Risk Assessment;toxicity.

  2. Analysing breast cancer microarrays from African Americans using shrinkage-based discriminant analysis

    Directory of Open Access Journals (Sweden)

    Pang Herbert

    2010-10-01

    Full Text Available Abstract Breast cancer tumours among African Americans are usually more aggressive than those found in Caucasian populations. African-American patients with breast cancer also have higher mortality rates than Caucasian women. A better understanding of the disease aetiology of these breast cancers can help to improve and develop new methods for cancer prevention, diagnosis and treatment. The main goal of this project was to identify genes that help differentiate between oestrogen receptor-positive and -negative samples among a small group of African-American patients with breast cancer. Breast cancer microarrays from one of the largest genomic consortiums were analysed using 13 African-American and 201 Caucasian samples with oestrogen receptor status. We used a shrinkage-based classification method to identify genes that were informative in discriminating between oestrogen receptor-positive and -negative samples. Subset analysis and permutation were performed to obtain a set of genes unique to the African-American population. We identified a set of 156 probe sets, which gave a misclassification rate of 0.16 in distinguishing between oestrogen receptor-positive and -negative patients. The biological relevance of our findings was explored through literature-mining techniques and pathway mapping. An independent dataset was used to validate our findings and we found that the top ten genes mapped onto this dataset gave a misclassification rate of 0.15. The described method allows us best to utilise the information available from small sample size microarray data in the context of ethnic minorities.

  3. Proteomics Analysis for Finding Serum Markers of Ovarian Cancer

    Directory of Open Access Journals (Sweden)

    Yushan Cheng

    2014-01-01

    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.

  4. Survival Analysis of Breast Cancer Subtypes in Patients With Spinal Metastases

    DEFF Research Database (Denmark)

    Wang, Miao; Jensen, Anders Bonde; Morgen, Soeren Smith;

    2014-01-01

    in determining breast cancer subtypes and predicting patients' response to adjuvant treatments. METHODS: Until August 2013, we retrieved 151 surgically treated patients with breast cancer spinal metastases and followed up all the patients for at least 2 years. Survival duration analysis and Cox proportional...... hazards regression model unadjusted and adjusted by age were used. RESULTS: Patients with ER-negative (-) breast cancer had 11 months shorter median survival duration (10.6 vs. 21.5 mo) and 48% higher mortality risk (P=0.03) than those with ER-positive (+) breast cancer. Patients with PgR (-) status had...... from score "5" to "3" in Tokuhashi scoring system and from "slow growth" to "moderate growth" in Tomita scoring system. Spine surgeons should be critical before performing high-risk extensive surgery in patients with ER/HR (-) status, and especially, in those with triple-negative status. LEVEL...

  5. Integrated genomic analysis of breast cancers.

    Science.gov (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

    2012-12-01

    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

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

    Directory of Open Access Journals (Sweden)

    Catarina Aparecida Sales

    2014-10-01

    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.

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    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...... 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...

  8. Evaluation of algorithm methods for fluorescence spectra of cancerous and normal human tissues

    Science.gov (United States)

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

    2016-03-01

    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

  9. 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)

    2016-09-27

    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.

  10. 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

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

    Directory of Open Access Journals (Sweden)

    Andrew E Teschendorff

    2007-08-01

    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.

  12. Association of XPC polymorphisms and lung cancer risk: a meta-analysis.

    Directory of Open Access Journals (Sweden)

    Bo Jin

    Full Text Available BACKGROUND: Xeroderma pigmentosum complementation group C gene (XPC is a key member of nucleotide excision repair pathway and plays an important role in human DNA repair system. It is reported that several common polymorphisms of XPC are associated with susceptibility to lung cancer. However, the conclusion is still elusive. METHOD: This meta-analysis was performed to determine the relationship between XPC polymorphisms (Lys939Gln, Ala499Val, and PAT and lung cancer risk. Published literatures were identified by searching online databases and reference lists of relevant studies. Odds ratios (ORs and 95% confidence intervals (CIs were calculated to estimate the association strength. Publication bias were detected by Egger's and Begg's test. RESULT: After strict screening, we identified 14 eligible studies in this meta-analysis, including 5647 lung cancer cases and 6908 controls. By pooling all eligible studies, we found that the homozygote Gln939Gln genotype was associated with a significantly increased risk of lung cancer in Asian population (GlnGln vs LysLys, OR=1.229, 95% CI: 1.000-1.510; GlnGln vs LysLys/LysGln, OR=1.257, 95% CI: 1.038-1.522. As for the PAT polymorphism, in Caucasian population, we found carriers of the -/- genotype were associated significantly reduced risk of lung cancer in homozygote comparison model (-/- vs +/+, OR=0.735, 95% CI: 0.567-0.952. CONCLUSION: In this meta-analysis we found that Gln939Gln genotype was associated with significantly increased risk of lung cancer in Asian population; the PAT -/- genotype significantly reduced susceptibility to lung cancer in Caucasian population; while the XPC Ala499Val polymorphism was not associated with lung cancer risk.

  13. 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.

  14. 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

    2008-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Ma GX

    2012-05-01

    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

  16. An introduction to numerical methods and analysis

    CERN Document Server

    Epperson, James F

    2013-01-01

    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

  17. CRYOGENIC TREATMENT FOR CANCER OF THE TONGUE AND ORAL CAVITY (ANALYSIS OF ITS EFFICIENCY ACCORDING TO SURVIVAL RATES IN THE PERIOD 1975–2009)

    OpenAIRE

    T. D. Tabolinovskaya

    2013-01-01

    Case histories of 366 patients with cancer of the oral mucosa, tongue, and oropharynx who had received cryogenic treatment at the N.N. Blokhin Russian Cancer Research Center in the period 1975 to 2009 served as the material for the investigation. Analysis of the longterm results of cryogenic treatment for primary and recurrent cancers and tumors untreated after traditional treatments showed the efficiency of this method in 75.8 and 48.2 % of primary and recurrent cancer patients, respectively...

  18. Development and application of statistical methods for population-based cancer patient survival

    OpenAIRE

    Eloranta, Sandra

    2013-01-01

    The overarching aim of this work has been to develop and apply statistical methods for estimating cancer patient survival from population-based register data. Particular focus has been on statistical methods that can be used for presenting cancer survival statistics from administrative health data registers in a manner that is relevant for physicians and patients. Study 1: In this study we clarify and discuss the relative merits of estimates of crude and net cancer patient survival, resp...

  19. Spatial-temporal analysis of breast cancer in upper Cape Cod, Massachusetts

    Directory of Open Access Journals (Sweden)

    Aschengrau Ann

    2008-08-01

    Full Text Available Abstract Introduction The reasons for elevated breast cancer rates in the upper Cape Cod area of Massachusetts remain unknown despite several epidemiological studies that investigated possible environmental risk factors. Data from two of these population-based case-control studies provide geocoded residential histories and information on confounders, creating an invaluable dataset for spatial-temporal analysis of participants' residency over five decades. Methods The combination of statistical modeling and mapping is a powerful tool for visualizing disease risk in a spatial-temporal analysis. Advances in geographic information systems (GIS enable spatial analytic techniques in public health studies previously not feasible. Generalized additive models (GAMs are an effective approach for modeling spatial and temporal distributions of data, combining a number of desirable features including smoothing of geographical location, residency duration, or calendar years; the ability to estimate odds ratios (ORs while adjusting for confounders; selection of optimum degree of smoothing (span size; hypothesis testing; and use of standard software. We conducted a spatial-temporal analysis of breast cancer case-control data using GAMs and GIS to determine the association between participants' residential history during 1947–1993 and the risk of breast cancer diagnosis during 1983–1993. We considered geographic location alone in a two-dimensional space-only analysis. Calendar year, represented by the earliest year a participant lived in the study area, and residency duration in the study area were modeled individually in one-dimensional time-only analyses, and together in a two-dimensional time-only analysis. We also analyzed space and time together by applying a two-dimensional GAM for location to datasets of overlapping calendar years. The resulting series of maps created a movie which allowed us to visualize changes in magnitude, geographic size, and

  20. An Analysis Method of Business Application Framework

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    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 .

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

    Institute of Scientific and Technical Information of China (English)

    LU LI; TONG-DA SUN; XING ZHANG; RUI-NAN LAI; XIU-YANG LI; XUE-JIN FAN; KENJI MORINAGA

    2004-01-01

    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.

  2. Association between MGMT Promoter Methylation and Non-Small Cell Lung Cancer: A Meta-Analysis

    OpenAIRE

    Changmei Gu; Jiachun Lu; Tianpen Cui; Cheng Lu; Hao Shi; Wenmao Xu; Xueli Yuan; Xiaobo Yang; Yangxin Huang; Meixia Lu

    2013-01-01

    BACKGROUND: O(6)-methylguanine-DNA methyltransferase (MGMT) is one of most important DNA repair enzyme against common carcinogens such as alkylate and tobacco. Aberrant promoter methylation of the gene is frequently observed in non-small cell lung cancer (NSCLC). However, the importance of epigenetic inactivation of the gene in NSCLC published in the literature showed inconsistence. We quantified the association between MGMT promoter methylation and NSCLC using a meta-analysis method. METHODS...

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

    Directory of Open Access Journals (Sweden)

    Kamila Schmidt

    2015-01-01

    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.

  4. Does colon cancer ever metastasize to bone first? a temporal analysis of colorectal cancer progression

    International Nuclear Information System (INIS)

    It is well recognized that colorectal cancer does not frequently metastasize to bone. The aim of this retrospective study was to establish whether colorectal cancer ever bypasses other organs and metastasizes directly to bone and whether the presence of lung lesions is superior to liver as a better predictor of the likelihood and timing of bone metastasis. We performed a retrospective analysis on patients with a clinical diagnosis of colon cancer referred for staging using whole-body 18F-FDG PET and CT or PET/CT. We combined PET and CT reports from 252 individuals with information concerning patient history, other imaging modalities, and treatments to analyze disease progression. No patient had isolated osseous metastasis at the time of diagnosis, and none developed isolated bone metastasis without other organ involvement during our survey period. It took significantly longer for colorectal cancer patients to develop metastasis to the lungs (23.3 months) or to bone (21.2 months) than to the liver (9.8 months). Conclusion: Metastasis only to bone without other organ involvement in colorectal cancer patients is extremely rare, perhaps more rare than we previously thought. Our findings suggest that resistant metastasis to the lungs predicts potential disease progression to bone in the colorectal cancer population better than liver metastasis does

  5. Biomedical Engineering 2008. New methods for cancer treatment

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-07-01

    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

  6. Causal Moderation Analysis Using Propensity Score Methods

    Science.gov (United States)

    Dong, Nianbo

    2012-01-01

    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…

  7. ANALYSIS OF MODERN CAR BODY STRAIGHTENING METHODS

    Directory of Open Access Journals (Sweden)

    Arhun, Sch.

    2013-01-01

    Full Text Available The analysis of modern car body panels straightening methods is carried out. There have been described both traditional and alternative methods of car body panels straightening. The urgency of magnetic pulse teсhnology dignment is grounded. The main advantages of magnetic pulse teсhno-logy of car body straightening are defernined.

  8. Relating Actor Analysis Methods to Policy Problems

    NARCIS (Netherlands)

    Van der Lei, T.E.

    2009-01-01

    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

  9. Empirical likelihood method in survival analysis

    CERN Document Server

    Zhou, Mai

    2015-01-01

    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

  10. 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

    2016-01-01

    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.

  11. Digital image analysis outperforms manual biomarker assessment in breast cancer.

    Science.gov (United States)

    Stålhammar, Gustav; Fuentes Martinez, Nelson; Lippert, Michael; Tobin, Nicholas P; Mølholm, Ida; Kis, Lorand; Rosin, Gustaf; Rantalainen, Mattias; Pedersen, Lars; Bergh, Jonas; Grunkin, Michael; Hartman, Johan

    2016-04-01

    In the spectrum of breast cancers, categorization according to the four gene expression-based subtypes 'Luminal A,' 'Luminal B,' 'HER2-enriched,' and 'Basal-like' is the method of choice for prognostic and predictive value. As gene expression assays are not yet universally available, routine immunohistochemical stains act as surrogate markers for these subtypes. Thus, congruence of surrogate markers and gene expression tests is of utmost importance. In this study, 3 cohorts of primary breast cancer specimens (total n=436) with up to 28 years of survival data were scored for Ki67, ER, PR, and HER2 status manually and by digital image analysis (DIA). The results were then compared for sensitivity and specificity for the Luminal B subtype, concordance to PAM50 assays in subtype classification and prognostic power. The DIA system used was the Visiopharm Integrator System. DIA outperformed manual scoring in terms of sensitivity and specificity for the Luminal B subtype, widely considered the most challenging distinction in surrogate subclassification, and produced slightly better concordance and Cohen's κ agreement with PAM50 gene expression assays. Manual biomarker scores and DIA essentially matched each other for Cox regression hazard ratios for all-cause mortality. When the Nottingham combined histologic grade (Elston-Ellis) was used as a prognostic surrogate, stronger Spearman's rank-order correlations were produced by DIA. Prognostic value of Ki67 scores in terms of likelihood ratio χ(2) (LR χ(2)) was higher for DIA that also added significantly more prognostic information to the manual scores (LR-Δχ(2)). In conclusion, the system for DIA evaluated here was in most aspects a superior alternative to manual biomarker scoring. It also has the potential to reduce time consumption for pathologists, as many of the steps in the workflow are either automatic or feasible to manage without pathological expertise. PMID:26916072

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

    Directory of Open Access Journals (Sweden)

    Mahjub H

    2006-01-01

    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.

  13. Quantitative analysis of cell-free DNA in ovarian cancer

    Science.gov (United States)

    SHAO, XUEFENG; He, YAN; JI, MIN; CHEN, XIAOFANG; QI, JING; SHI, WEI; HAO, TIANBO; JU, SHAOQING

    2015-01-01

    The aim of the present study was to investigate the association between cell-free DNA (cf-DNA) levels and clinicopathological characteristics of patients with ovarian cancer using a branched DNA (bDNA) technique, and to determine the value of quantitative cf-DNA detection in assisting with the diagnosis of ovarian cancer. Serum specimens were collected from 36 patients with ovarian cancer on days 1, 3 and 7 following surgery, and additional serum samples were also collected from 22 benign ovarian tumor cases, and 19 healthy, non-cancerous ovaries. bDNA techniques were used to detect serum cf-DNA concentrations. All data were analyzed using SPSS version 18.0. The cf-DNA levels were significantly increased in the ovarian cancer group compared with those of the benign ovarian tumor group and healthy ovarian group (P<0.01). Furthermore, cf-DNA levels were significantly increased in stage III and IV ovarian cancer compared with those of stages I and II (P<0.01). In addition, cf-DNA levels were significantly increased on the first day post-surgery (P<0.01), and subsequently demonstrated a gradual decrease. In the ovarian cancer group, the area under the receiver operating characteristic curve of cf-DNA and the sensitivity were 0.917 and 88.9%, respectively, which was higher than those of cancer antigen 125 (0.724, 75%) and human epididymis protein 4 (0.743, 80.6%). There was a correlation between the levels of serum cf-DNA and the occurrence and development of ovarian cancer in the patients evaluated. bDNA techniques possessed higher sensitivity and specificity than other methods for the detection of serum cf-DNA in patients exhibiting ovarian cancer, and bDNA techniques are more useful for detecting cf-DNA than other factors. Thus, the present study demonstrated the potential value for the use of bDNA as an adjuvant diagnostic method for ovarian cancer. PMID:26788153

  14. Excitation methods for energy dispersive analysis

    International Nuclear Information System (INIS)

    The rapid development in recent years of energy dispersive x-ray fluorescence analysis has been based primarily on improvements in semiconductor detector x-ray spectrometers. However, the whole analysis system performance is critically dependent on the availability of optimum methods of excitation for the characteristic x rays in specimens. A number of analysis facilities based on various methods of excitation have been developed over the past few years. A discussion is given of the features of various excitation methods including charged particles, monochromatic photons, and broad-energy band photons. The effects of the excitation method on background and sensitivity are discussed from both theoretical and experimental viewpoints. Recent developments such as pulsed excitation and polarized photons are also discussed

  15. Evaluation of prostate cancer antigen 3 for detecting prostate cancer: a systematic review and meta-analysis

    Science.gov (United States)

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

    2016-05-01

    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.

  16. Emotions and coping of patients with head and neck cancers after diagnosis: A qualitative content analysis

    Directory of Open Access Journals (Sweden)

    A Jagannathan

    2016-01-01

    Full Text Available Background and Rationale: Patients suffering with head and neck cancers are observed to have a relatively high risk of developing emotional disturbances after diagnosis and treatment. These emotional concerns can be best understood and explored through the method of content analysis or qualitative data. Though a number of qualitative studies have been conducted in the last few years in the field of psychosocial oncology, none have looked at the emotions experienced and the coping by head and neck cancer patients. Materials and Methods: Seventy-five new cases of postsurgery patients of head and neck cancers were qualitatively interviewed regarding the emotions experienced and coping strategies after diagnosis. Results: Qualitative content analysis of the in-depth interviews brought out that patients experienced varied emotions on realizing that they were suffering from cancer, the cause of which could be mainly attributed to three themes: 1 knowledge of their illness; 2 duration of untreated illness; and 3 object of blame. They coped with their emotions by either: 1 inculcating a positive attitude and faith in the doctor/treatment, 2 ventilating their emotions with family and friends, or 3 indulging in activities to divert attention. Conclusion: The results brought out a conceptual framework, which showed that an in-depth understanding of the emotions - Their root cause, coping strategies, and spiritual and cultural orientations of the cancer survivor - Is essential to develop any effective intervention program in India.

  17. Scope-Based Method Cache Analysis

    DEFF Research Database (Denmark)

    Huber, Benedikt; Hepp, Stefan; Schoeberl, Martin

    2014-01-01

    , 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...

  18. Genomic analysis and selected molecular pathways in rare cancers

    International Nuclear Information System (INIS)

    It is widely accepted that many cancers arise as a result of an acquired genomic instability and the subsequent evolution of tumor cells with variable patterns of selected and background aberrations. The presence and behaviors of distinct neoplastic cell populations within a patient's tumor may underlie multiple clinical phenotypes in cancers. A goal of many current cancer genome studies is the identification of recurring selected driver events that can be advanced for the development of personalized therapies. Unfortunately, in the majority of rare tumors, this type of analysis can be particularly challenging. Large series of specimens for analysis are simply not available, allowing recurring patterns to remain hidden. In this paper, we highlight the use of DNA content-based flow sorting to identify and isolate DNA-diploid and DNA-aneuploid populations from tumor biopsies as a strategy to comprehensively study the genomic composition and behaviors of individual cancers in a series of rare solid tumors: intrahepatic cholangiocarcinoma, anal carcinoma, adrenal leiomyosarcoma, and pancreatic neuroendocrine tumors. We propose that the identification of highly selected genomic events in distinct tumor populations within each tumor can identify candidate driver events that can facilitate the development of novel, personalized treatment strategies for patients with cancer. (paper)

  19. 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

    2011-01-01

    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

  20. Dynamic infrared imaging in identification of breast cancer tissue with combined image processing and frequency analysis.

    Science.gov (United States)

    Joro, R; Lääperi, A-L; Soimakallio, S; Järvenpää, R; Kuukasjärvi, T; Toivonen, T; Saaristo, R; Dastidar, P

    2008-01-01

    Five combinations of image-processing algorithms were applied to dynamic infrared (IR) images of six breast cancer patients preoperatively to establish optimal enhancement of cancer tissue before frequency analysis. mid-wave photovoltaic (PV) IR cameras with 320x254 and 640x512 pixels were used. The signal-to-noise ratio and the specificity for breast cancer were evaluated with the image-processing combinations from the image series of each patient. Before image processing and frequency analysis the effect of patient movement was minimized with a stabilization program developed and tested in the study by stabilizing image slices using surface markers set as measurement points on the skin of the imaged breast. A mathematical equation for superiority value was developed for comparison of the key ratios of the image-processing combinations. The ability of each combination to locate the mammography finding of breast cancer in each patient was compared. Our results show that data collected with a 640x512-pixel mid-wave PV camera applying image-processing methods optimizing signal-to-noise ratio, morphological image processing and linear image restoration before frequency analysis possess the greatest superiority value, showing the cancer area most clearly also in the match centre of the mammography estimation. PMID:18666012

  1. The Spatial Distribution of Cancer Incidence in Fars Province: A GIS-Based Analysis of Cancer Registry Data

    OpenAIRE

    Ali Goli; Mahbobeh Oroei; Mehdi Jalalpour; Hossein Faramarzi; Mehrdad Askarian

    2013-01-01

    Background: Cancer is a major health problem in the developing countries. Variations of its incidence rate among geographical areas are due to various contributing factors. This study was performed to assess the spatial patterns of cancer incidence in the Fars Province, based on cancer registry data and to determine geographical clusters. Methods: In this cross sectional study, the new cases of cancer were recorded from 2001 to 2009. Crude incidence rate was estimated based on age groups ...

  2. 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

    2015-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Feriel Sellam

    2008-09-01

    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.

  4. A minimum spanning forest based hyperspectral image classification method for cancerous tissue detection

    Science.gov (United States)

    Pike, Robert; Patton, Samuel K.; Lu, Guolan; Halig, Luma V.; Wang, Dongsheng; Chen, Zhuo Georgia; Fei, Baowei

    2014-03-01

    Hyperspectral imaging is a developing modality for cancer detection. The rich information associated with hyperspectral images allow for the examination between cancerous and healthy tissue. This study focuses on a new method that incorporates support vector machines into a minimum spanning forest algorithm for differentiating cancerous tissue from normal tissue. Spectral information was gathered to test the algorithm. Animal experiments were performed and hyperspectral images were acquired from tumor-bearing mice. In vivo imaging experimental results demonstrate the applicability of the proposed classification method for cancer tissue classification on hyperspectral images.

  5. Machine learning methods in the computational biology of cancer.

    Science.gov (United States)

    Vidyasagar, M

    2014-07-01

    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.

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

    Directory of Open Access Journals (Sweden)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    Kiyohara, Chikako, E-mail: chikako@phealth.med.kyushu-u.ac.jp [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)

    2010-10-28

    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

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

    International Nuclear Information System (INIS)

    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

  9. Prognostic Value of MicroRNA-182 in Cancers: A Meta-Analysis

    OpenAIRE

    2015-01-01

    Objective. MicroRNA-182 (miR-182) exhibits altered expression in various cancers. The aim of this study was to investigate the predictive value of miR-182 expression for cancer patient survival. Methods. Eligible studies were identified through multiple search strategies, and the hazard ratios (HRs) for patient outcomes were extracted and estimated. A meta-analysis was performed to evaluate the prognostic value of miR-182. Results. In total, 14 studies were included. A high miR-182 expression...

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

    Directory of Open Access Journals (Sweden)

    Jian ZHU

    2011-01-01

    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.

  11. Bisphosphonate use and gastrointestinal tract cancer risk:Meta-analysis of observational studies

    Institute of Scientific and Technical Information of China (English)

    Yun Hwan Oh; Chan Yoon; Sang Min Park

    2012-01-01

    AIM:To perform a meta-analysis of observational studies to further elucidate the relationship between oral bisphosphonate use and gastrointestinal cancer risk.METHODS:Systematic literature search was conducted in MEDLINE,EMBASE,and the Cochrane Library to identify studies through January 2011.Search terms were "bisphosphonates" or trade names of the drugs,and "observational studies" or "cohort studies" or "case-control studies".Two evaluators reviewed and selected articles on the basis of predetermined selection criteria as followed:(1) observational studies (casecontrol or cohort studies) on bisphosphonate use; (2)with at least 2 years of follow-up; and (3) reported data on the incidence of cancer diagnosis.The DerSimonian and Laird random effects model were used to calculate the pooled relative risk (RR) with 95% confidence interval (CI).Two-by-two contingency table was used to calculate the outcomes not suitable for meta-analysis.Subgroup meta-analyses were conducted for the type of cancer (esophageal,gastric and colorectal cancers).Sensitivity analyses were performed to examine the effect sizes when only studies with long-term follow-up (mean 5 years; subgroup 3 years) were included.RESULTS:Of 740 screened articles,3 cohort studies and 3 case-control studies were included in the analyses.At first,4 cohort studies and 3 case-control studies were selected for the analyses but one cohort study was excluded because the cancer outcomes were not categorized by type of gastrointestinal cancer.More than 124 686 subjects participated in the 3 cohort studies.The mean follow-up time in all of the cohort studies combined was approximately 3.88 years.The 3 casecontrol studies reported 3070 esophageal cancer cases and 15 417 controls,2018 gastric cancer cases and 10 007 controls,and 11 574 colorectal cancer cases and 53 955 controls.The percentage of study participants who used bisphosphonate was 2.8% among the cases and 2.9% among the controls.The meta-analysis of all

  12. 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.

  13. ANALYSIS OF THE EFFICIENCY OF CRYOGENIC TREATMENT FOR TONGUE CANCER

    OpenAIRE

    T. D. Tabolinovskaya; I. N. Pustynsky

    2014-01-01

    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 an...

  14. Gene expression analysis of FABP4 in gastric cancer

    OpenAIRE

    Abdulkarim Yasin Karim

    2016-01-01

    Purpose: Gastric cancer has high incidence and mortality rate in several countries and is still one of the most frequent and lethal disease. In this study, we aimed to determine diagnostic markers in gastric cancer by molecular techniques; include mRNA expression analysis of FABP4 gene. Fatty acid binding protein 4 (FABP4) gene encodes the fatty acid binding protein found in adipocytes. The protein encoded by FABP4 are a family of small, highly conserved, cytoplasmic proteins that bind long-c...

  15. 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.

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

    Directory of Open Access Journals (Sweden)

    Guru Trikudanathan

    2011-01-01

    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.

  17. Genes-environment interactions in obesity- and diabetes-associated pancreatic cancer: A GWAS data analysis

    Science.gov (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

    2013-01-01

    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

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

    Directory of Open Access Journals (Sweden)

    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.

  19. Coffee and gastric cancer: systematic review and meta-analysis

    Directory of Open Access Journals (Sweden)

    Botelho Francisco

    2006-01-01

    Full Text Available We systematically reviewed the literature on the association between coffee consumption and gastric cancer and performed a meta-analysis of the results. Published cohort and case-control studies were identified in PubMed and reference lists. Random effects meta-analysis was used to pool effects from 23 studies, and heterogeneity was explored by stratification and meta-regression. The odds ratio (OR for the overall association between coffee and gastric cancer (highest vs. lowest category of exposure was 0.97 (95%CI: 0.86-1.09, similar for cohort (OR = 1.02; 95%CI: 0.76-1.37 and case-control studies (population-based: OR = 0.90; 95%CI: 0.70-1.15; hospital-based: OR = 0.97; 95%CI: 0.83-1.13. The OR was 1.26 (95%CI: 1.02-1.57 when considering five studies conducted in the USA, 0.97 (95%CI: 0.82-1.14 for the five Japanese studies, 0.98 (95%CI: 0.81-1.17 for the six studies from Europe, and 0.64 (95%CI: 0.47-0.86 for the two studies from South America. In this meta-analysis we found no adverse effect of coffee associated with gastric cancer. Knowledge on the level of exposure to different coffee constituents may provide a deeper understanding of this reassuring result and the real role of coffee on cancer risk.

  20. Coffee and gastric cancer: systematic review and meta-analysis.

    Science.gov (United States)

    Botelho, Francisco; Lunet, Nuno; Barros, Henrique

    2006-05-01

    We systematically reviewed the literature on the association between coffee consumption and gastric cancer and performed a meta-analysis of the results. Published cohort and case-control studies were identified in PubMed and reference lists. Random effects meta-analysis was used to pool effects from 23 studies, and heterogeneity was explored by stratification and meta-regression. The odds ratio (OR) for the overall association between coffee and gastric cancer (highest vs. lowest category of exposure) was 0.97 (95%CI: 0.86-1.09), similar for cohort (OR = 1.02; 95%CI: 0.76-1.37) and case-control studies (population-based: OR = 0.90; 95%CI: 0.70-1.15; hospital-based: OR = 0.97; 95%CI: 0.83-1.13). The OR was 1.26 (95%CI: 1.02-1.57) when considering five studies conducted in the USA, 0.97 (95%CI: 0.82-1.14) for the five Japanese studies, 0.98 (95%CI: 0.81-1.17) for the six studies from Europe, and 0.64 (95%CI: 0.47-0.86) for the two studies from South America. In this meta-analysis we found no adverse effect of coffee associated with gastric cancer. Knowledge on the level of exposure to different coffee constituents may provide a deeper understanding of this reassuring result and the real role of coffee on cancer risk. PMID:16680342

  1. Coffee and gastric cancer: systematic review and meta-analysis

    Directory of Open Access Journals (Sweden)

    Francisco Botelho

    2006-05-01

    Full Text Available We systematically reviewed the literature on the association between coffee consumption and gastric cancer and performed a meta-analysis of the results. Published cohort and case-control studies were identified in PubMed and reference lists. Random effects meta-analysis was used to pool effects from 23 studies, and heterogeneity was explored by stratification and meta-regression. The odds ratio (OR for the overall association between coffee and gastric cancer (highest vs. lowest category of exposure was 0.97 (95%CI: 0.86-1.09, similar for cohort (OR = 1.02; 95%CI: 0.76-1.37 and case-control studies (population-based: OR = 0.90; 95%CI: 0.70-1.15; hospital-based: OR = 0.97; 95%CI: 0.83-1.13. The OR was 1.26 (95%CI: 1.02-1.57 when considering five studies conducted in the USA, 0.97 (95%CI: 0.82-1.14 for the five Japanese studies, 0.98 (95%CI: 0.81-1.17 for the six studies from Europe, and 0.64 (95%CI: 0.47-0.86 for the two studies from South America. In this meta-analysis we found no adverse effect of coffee associated with gastric cancer. Knowledge on the level of exposure to different coffee constituents may provide a deeper understanding of this reassuring result and the real role of coffee on cancer risk.

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

    Science.gov (United States)

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

    2016-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Mariya A. Qurieshi

    2016-01-01

    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.

  4. Advanced analysis methods in particle physics

    Energy Technology Data Exchange (ETDEWEB)

    Bhat, Pushpalatha C.; /Fermilab

    2010-10-01

    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.

  5. Algorithmic methods to infer the evolutionary trajectories in cancer progression

    OpenAIRE

    Caravagna, Giulio; Graudenzi, Alex; Ramazzotti, Daniele; Sanz-Pamplona, Rebeca; De Sano, Luca; Mauri, Giancarlo; Moreno, Victor; Antoniotti, Marco; Mishra, Bud

    2016-01-01

    The genomic evolution inherent to cancer relates directly to a renewed focus on the voluminous next generation sequencing (NGS) data, and machine learning for the inference of explanatory models of how the (epi)genomic events are choreographed in cancer initiation and development. However, despite the increasing availability of multiple additional -omics data, this quest has been frustrated by various theoretical and technical hurdles, mostly stemming from the dramatic heterogeneity of the di...

  6. A historical discourse analysis of the cancerous and non-cancerous body in secondary biology textbooks

    Science.gov (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

  7. 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

  8. 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

    2014-01-01

    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.

  9. Analysis of mixed data methods & applications

    CERN Document Server

    de Leon, Alexander R

    2013-01-01

    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

  10. Egg consumption and breast cancer risk: a meta-analysis.

    Science.gov (United States)

    Si, Ruohuang; Qu, Kunpeng; Jiang, Zebin; Yang, Xiaojun; Gao, Peng

    2014-05-01

    The relationship between egg consumption and breast cancer risk has been inconsistent, so it is necessary to conduct a meta-analysis to evaluate the relationship. PubMed, EMBASE and ISI Web of Knowledge were searched to find cohort studies or case control studies that evaluated the relationship between egg consumption and breast cancer risk. A comprehensive meta-analysis software was used to conduct the meta-analysis. 13 studies were included. The meta-analysis results showed that egg consumption was associated with increased breast cancer risk (RR 1.04, 95 % CI 1.01-1.08). Subgroup analyses showed egg consumption was also associated with increased breast cancer risk based on cohort studies (RR 1.04, 95 % CI 1.00-1.08), among European population (RR 1.05, 95 % CI 1.01-1.09), Asian population (RR 1.09, 95 % CI 1.00-1.18), postmenopausal population (RR 1.06, 95 % CI 1.02-1.10), and those who consumed ≥2, ≤5/week (RR 1.10, 95 % CI 1.02-1.17), but not in case-control studies (RR 1.06, 95 % CI 0.97-1.15), among American population (RR 1.04, 95 % CI 0.94-1.16), premenopausal population (RR 1.04, 95 % CI 0.98-1.11) and those who consumed ≥1, 5 eggs/week (RR 0.97, 95 % CI 0.88-1.06). Egg consumption was associated with increased breast cancer risk among the European, Asian and postmenopausal population and those who consumed ≥2, ≤5/week. PMID:24504557

  11. ANALYSIS OF THE EFFICIENCY OF CRYOGENIC TREATMENT FOR TONGUE CANCER

    Directory of Open Access Journals (Sweden)

    T. D. Tabolinovskaya

    2014-01-01

    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.

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

    Science.gov (United States)

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

    2015-01-01

    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. PMID:25826459

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

    Science.gov (United States)

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

    2015-01-01

    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.

  14. 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.

  15. Chromatographic methods for analysis of triazine herbicides.

    Science.gov (United States)

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

    2015-01-01

    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. PMID:25849823

  16. Chromatographic methods for analysis of triazine herbicides.

    Science.gov (United States)

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

    2015-01-01

    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. Microfluidic Exosome Analysis toward Liquid Biopsy for Cancer.

    Science.gov (United States)

    He, Mei; Zeng, Yong

    2016-08-01

    Assessment of a tumor's molecular makeup using biofluid samples, known as liquid biopsy, is a prominent research topic in precision medicine for cancer, due to its noninvasive property allowing repeat sampling for monitoring molecular changes of tumors over time. Circulating exosomes recently have been recognized as promising tumor surrogates because they deliver enriched biomarkers, such as proteins, RNAs, and DNA. However, purification and characterization of these exosomes are technically challenging. Microfluidic lab-on-a-chip technology effectively addresses these challenges owing to its inherent advantages in integration and automation of multiple functional modules, enhancing sensing performance, and expediting analysis processes. In this article, we review the state-of-the-art development of microfluidic technologies for exosome isolation and molecular characterization with emphasis on their applications toward liquid biopsy-based analysis of cancer. Finally, we share our perspectives on current challenges and future directions of microfluidic exosome analysis. PMID:27215792

  18. Review of strain buckling: analysis methods

    International Nuclear Information System (INIS)

    This report represents an attempt to review the mechanical analysis methods reported in the literature to account for the specific behaviour that we call buckling under strain. In this report, this expression covers all buckling mechanisms in which the strains imposed play a role, whether they act alone (as in simple buckling under controlled strain), or whether they act with other loadings (primary loading, such as pressure, for example). Attention is focused on the practical problems relevant to LMFBR reactors. The components concerned are distinguished by their high slenderness ratios and by rather high thermal levels, both constant and variable with time. Conventional static buckling analysis methods are not always appropriate for the consideration of buckling under strain. New methods must therefore be developed in certain cases. It is also hoped that this review will facilitate the coding of these analytical methods to aid the constructor in his design task and to identify the areas which merit further investigation

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

    Directory of Open Access Journals (Sweden)

    Ruchi Bhandari

    2014-01-01

    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.

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

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    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.

  1. Evaluation of image guided motion management methods in lung cancer radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Zhuang, Ling [Department of Radiation Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, Michigan 48201 (United States); Yan, Di; Liang, Jian; Ionascu, Dan; Mangona, Victor; Yang, Kai; Zhou, Jun, E-mail: jun.zhou@beaumont.edu [Department of Radiation Oncology, William Beaumont Hospital, 3601 West Thirteen Mile Road, Royal Oak, Michigan 48073 (United States)

    2014-03-15

    Purpose: To evaluate the accuracy and reliability of three target localization methods for image guided motion management in lung cancer radiotherapy. Methods: Three online image localization methods, including (1) 2D method based on 2D cone beam (CB) projection images, (2) 3D method using 3D cone beam CT (CBCT) imaging, and (3) 4D method using 4D CBCT imaging, have been evaluated using a moving phantom controlled by (a) 1D theoretical breathing motion curves and (b) 3D target motion patterns obtained from daily treatment of 3 lung cancer patients. While all methods are able to provide target mean position (MP), the 2D and 4D methods can also provide target motion standard deviation (SD) and excursion (EX). For each method, the detected MP/SD/EX values are compared to the analytically calculated actual values to calculate the errors. The MP errors are compared among three methods and the SD/EX errors are compared between the 2D and 4D methods. In the theoretical motion study (a), the dependency of MP/SD/EX error on EX is investigated with EX varying from 2.0 cm to 3.0 cm with an increment step of 0.2 cm. In the patient motion study (b), the dependency of MP error on target sizes (2.0 cm and 3.0 cm), motion patterns (four motions per patient) and EX variations is investigated using multivariant linear regression analysis. Results: In the theoretical motion study (a), the MP detection errors are −0.2 ± 0.2, −1.5 ± 1.1, and −0.2 ± 0.2 mm for 2D, 3D, and 4D methods, respectively. Both the 2D and 4D methods could accurately detect motion pattern EX (error < 1.2 mm) and SD (error < 1.0 mm). In the patient motion study (b), MP detection error vector (mm) with the 2D method (0.7 ± 0.4) is found to be significantly less than with the 3D method (1.7 ± 0.8,p < 0.001) and the 4D method (1.4 ± 1.0, p < 0.001) using paired t-test. However, no significant difference is found between the 4D method and the 3D method. Based on multivariant linear regression analysis, the

  2. An introduction to numerical methods and analysis

    CERN Document Server

    Epperson, J F

    2007-01-01

    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

  3. 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.

    2012-01-01

    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

  4. Consortium analysis of 7 candidate SNPs for ovarian cancer

    DEFF Research Database (Denmark)

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

    2008-01-01

    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...... was suggestive although no longer statistically significant (ordinal OR 0.92, 95% CI 0.79-1.06). This SNP has also been shown to have an association with decreased risk in breast cancer. There was a suggestion of an association for AURKA, when one study that caused significant study heterogeneity was excluded...... [ordinal OR 1.10 (95% CI 1.01-1.20) p = 0.027; dominant OR 1.12 (95% CI 1.01-1.24) p = 0.03]. The other 5 SNPs in BRCA2, CDKN2A, SRD5A2, CASP8 and TGFB1 showed no association with ovarian cancer risk; given the large sample size, these results can also be considered to be informative. These null results...

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

    Directory of Open Access Journals (Sweden)

    Shu-li ZHU

    2015-04-01

    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

  6. 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)

    2016-02-15

    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.)

  7. Analysis of colorectal cancers for human cytomegalovirus presence

    Directory of Open Access Journals (Sweden)

    Menestrina Fabio

    2009-04-01

    Full Text Available Abstract Background A possible association between human cytomegalovirus (HCMV infection and colorectal cancer progression has been inferred by the identification in tumour tissues of HCMV antigens and specific viral DNA or RNA sequences. To further investigate the relationship between HCMV and colorectal cancers we developed qualitative and quantitative PCR assay to detect HCMV DNA in 56 formalin-fixed paraffin-embedded (FFPE tissue samples from patients belonging to 4 different histological phenotypes: adenoma; poorly, moderately and well differentiated adenocarcinomas. Results Of the 56 FFPE tested tissue samples, 6 (11% were positive for HCMV nested PCR amplification, and more precisely 1 (5% of 20 cases of adenoma and 5 (21% of 24 cases of moderately differentiated adenocarcinoma. No PCR positivity was obtained in samples from well and poorly differentiated adenocarcinomas. Conclusion Our observations suggest that there is no evidence of a direct association between HCMV and colorectal cancer. Moreover, the results obtained are not supportive of a causal role of HCMV in the processes of carcinogenesis and/or progression of colorectal cancer. However, the fact that the virus may present a "hit and run" like-mechanism and HCMV can thus only be detectable at a particular stage of a processing adenocarcinoma, suggests that a significant number of colorectal cancers might have been the subject of HCMV infection that could contribute to trigger the oncogenic differentiation. Our analysis does not exclude the possibility of HCMV infection subsequent viral clearance.

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

    Directory of Open Access Journals (Sweden)

    Liu JW

    2015-12-01

    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

  9. 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

    2015-01-01

    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 (http://creativecommons.org/licenses/by-nc-nd/4.0/).

  10. 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

    2012-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Yanlai Sun

    2016-03-01

    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.

  12. The association between polycystic ovary syndrome and breast cancer: a meta-analysis

    Science.gov (United States)

    Shobeiri, Fatemeh

    2016-01-01

    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

  13. The association between polycystic ovary syndrome and breast cancer: a meta-analysis

    Science.gov (United States)

    Shobeiri, Fatemeh

    2016-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Maija Wolf

    2005-01-01

    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.

  15. Cancer risk in older people receiving statin therapy: a meta-analysis of randomized controlled trials

    Science.gov (United States)

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

    2016-01-01

    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.

  16. 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

    2012-01-01

    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.

  17. 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

    2014-03-01

    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.

  18. Numerical methods in software and analysis

    CERN Document Server

    Rice, John R

    1992-01-01

    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

  19. 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.

    2015-01-01

    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, and 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.

  20. 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.

    2015-01-02

    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.

  1. A new method for cancer detection based on diffusion reflection measurements of targeted gold nanorods

    Directory of Open Access Journals (Sweden)

    Ankri R

    2012-01-01

    Full Text Available Rinat Ankri, Vital Peretz, Menachem Motiei, Rachela Popovtzer, Dror FixlerFaculty of Engineering and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan 52900, IsraelAbstract: This paper presents a new method for cancer detection based on diffusion reflection measurements. This method enables discrimination between cancerous and noncancerous tissues due to the intense light absorption of gold nanorods (GNRs, which are selectively targeted to squamous cell carcinoma head and neck cancer cells. Presented in this paper are tissue-like phantom and in vivo results that demonstrate the high sensitivity of diffusion reflection measurements to the absorption differences between the GNR-targeted cancerous tissue and normal, noncancerous tissue. This noninvasive and nonionizing optical detection method provides a highly sensitive, simple, and inexpensive tool for cancer detection.Keywords: molecular imaging, nanoparticles, EGFR targeted, tissues’ optical properties

  2. Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis

    Directory of Open Access Journals (Sweden)

    Rogozin Igor B

    2006-02-01

    Full Text Available Abstract Background Carcinogenesis typically involves multiple somatic mutations in caretaker (DNA repair and gatekeeper (tumor suppressors and oncogenes genes. Analysis of mutation spectra of the tumor suppressor that is most commonly mutated in human cancers, p53, unexpectedly suggested that somatic evolution of the p53 gene during tumorigenesis is dominated by positive selection for gain of function. This conclusion is supported by accumulating experimental evidence of evolution of new functions of p53 in tumors. These findings prompted a genome-wide analysis of possible positive selection during tumor evolution. Methods A comprehensive analysis of probable somatic mutations in the sequences of Expressed Sequence Tags (ESTs from malignant tumors and normal tissues was performed in order to access the prevalence of positive selection in cancer evolution. For each EST, the numbers of synonymous and non-synonymous substitutions were calculated. In order to identify genes with a signature of positive selection in cancers, these numbers were compared to: i expected numbers and ii the numbers for the respective genes in the ESTs from normal tissues. Results We identified 112 genes with a signature of positive selection in cancers, i.e., a significantly elevated ratio of non-synonymous to synonymous substitutions, in tumors as compared to 37 such genes in an approximately equal-sized EST collection from normal tissues. A substantial fraction of the tumor-specific positive-selection candidates have experimentally demonstrated or strongly predicted links to cancer. Conclusion The results of EST analysis should be interpreted with extreme caution given the noise introduced by sequencing errors and undetected polymorphisms. Furthermore, an inherent limitation of EST analysis is that multiple mutations amenable to statistical analysis can be detected only in relatively highly expressed genes. Nevertheless, the present results suggest that positive

  3. [Treatment Ideas and Methods for Treating Breast Cancer Guided by Molecular Classification].

    Science.gov (United States)

    Wang, Hui-jie; Wang, Zhao-xia; Wan, Dong-gui; Li, Pei-wen

    2016-04-01

    The gene types of breast cancer can be classified into three types according to its molecules: Luminal type A, Luminal type B, HER-2-positive type, triple negative type. Authors combined pathological characteristics of breast cancer, biological characteristics, and comprehensive treatment, used syndrome typing based medication, and explored treatment meticulous ideas and methods of "treating the same disease with different methods" as well as "different treatment methods in accordance with patients individually". PMID:27323624

  4. Analysis of Pancreatic Cancer Microenvironment: Role of Macrophage Infiltrates and Growth Factors Expression

    Directory of Open Access Journals (Sweden)

    Katarzyna Gardian, Sława Janczewska, Waldemar L. Olszewski, Marek Durlik

    2012-01-01

    Full Text Available Background: Research over the last twenty years has yielded much insight into pancreatic cancer biology, but it has neither improved diagnostics methods nor the way of treatment. The question remains as to what the critical deciding factor is in making pancreatic cancer such an aggressive disease.Methods: Pancreatic tumor tissue came from 36 patients. To assess lymphatic vessels color lymphangiography and immunohistochemistry were used. Activity of matrix metalloproteinases was studied with gel and in situ zymography. Expression of growth factors and infiltrating immune cells were investigated using immunohistochemistry.Results: Our study revealed that the structures that correspond to lymphatic vessels were not observed in tumor center but only at the edge of the tumor. All studied growth factors were present in tumor tissue. We found that the difference in expression between G2 and G3 stage was statistically relevant in cases of c-Met receptor. Inflammatory cells were present around neoplastic glands and also strongly around nerves infiltrated by cancer cells. The number of infiltrating macrophages in tumor tissue was significantly higher in group with metastases to lymph nodes.Conclusion: We showed two factors that influence pancreatic cancer progression and invasion: c-Met receptors and macrophages infiltrating tumor tissue. Based on our analysis, this indicates that epithelial-mesenchymal transition might be crucial in the progression of pancreatic cancer.

  5. Practical Fourier analysis for multigrid methods

    CERN Document Server

    Wienands, Roman

    2004-01-01

    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...

  6. Multiple predictor smoothing methods for sensitivity analysis.

    Energy Technology Data Exchange (ETDEWEB)

    Helton, Jon Craig; Storlie, Curtis B.

    2006-08-01

    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.

  7. Reliability and risk analysis methods research plan

    International Nuclear Information System (INIS)

    This document presents a plan for reliability and risk analysis methods research to be performed mainly by the Reactor Risk Branch (RRB), Division of Risk Analysis and Operations (DRAO), Office of Nuclear Regulatory Research. It includes those activities of other DRAO branches which are very closely related to those of the RRB. Related or interfacing programs of other divisions, offices and organizations are merely indicated. The primary use of this document is envisioned as an NRC working document, covering about a 3-year period, to foster better coordination in reliability and risk analysis methods development between the offices of Nuclear Regulatory Research and Nuclear Reactor Regulation. It will also serve as an information source for contractors and others to more clearly understand the objectives, needs, programmatic activities and interfaces together with the overall logical structure of the program

  8. Sample Preparation for Mass Spectrometry Analysis of Protein-Protein Interactions in Cancer Cell Lines and Tissues.

    Science.gov (United States)

    Beigbeder, Alice; Vélot, Lauriane; James, D Andrew; Bisson, Nicolas

    2016-01-01

    A precisely controlled network of protein-protein interactions constitutes the basis for functional signaling pathways. This equilibrium is more often than not disrupted in cancer cells, by the aberrant expression or activation of oncogenic proteins. Therefore, the analysis of protein interaction networks in cancer cells has become crucial to expand our comprehension of the molecular underpinnings of tumor formation and progression. This protocol describes a sample preparation method for the analysis of signaling complexes by mass spectrometry (MS), following the affinity purification of a protein of interest from a cancer cell line or a solid tumor. In particular, we provide a spin tip-based protease digestion procedure that offers a more rapid and controlled alternative to other gel-based and gel-free methods. This sample preparation protocol represents a useful strategy to identify protein interactions and to gain insight into the molecular mechanisms that contribute to a given cancer phenotype. PMID:27581032

  9. Multivariate Analysis of Reproductive Risk Factors for Ovarian Cancer in Alexandria, Egypt

    International Nuclear Information System (INIS)

    Background: Ovarian cancer is the eighth leading cancer in women, as it accounts for 4% of all malignant tumors in females. The incidence of ovarian cancer is up to 10 times higher in western countries than in rural Asian and Africa ones. Different reproductive characteristics, life styles and specific medical conditions are responsible for different pattern and incidence of ovarian cancer worldwide. Material and Methods: A case control study was conducted during the time period from 2000 to 2003 including 172 cases of epithelial ovarian cancer, recently diagnosed and confirmed by histopathology. The patients were accessed at the hospitals currently covered by Alexandria Cancer Registry. In addition, 441 control subjects, comparable by age and address, were randomly selected from patients admitted to the same hospitals for non gynecological, non endocrinal acute diseases. Both cases and controls were subjected to a specific predesigned questionnaire to cover menstrual, reproductive and lifestyle indicators. Univariate and multivariate analysis were conducted and 5% level of significance was adopted. Results: Significantly increased risks were reported with increased number of abortions and increased number of ovarian cycles (OR=1.8, 95% CI (1.7-2.8), and 2.8, 95% CI 2.8 (1.5-5.2), respectively. Similarly, high risks were also reported for increased number of pregnancies, OR= 1.6, 95% CI 1.1-2.4) for I to three pregnancies and 4.2,95% CI 1.2-15.9) for more than four pregnancies On the other hand, decreased risks were reported for those with increased parity compared to nulliparous. Conclusion: Although ovarian cancer is less frequent in our community, yet the significant positive and negative associations between risk factors and ovarian cancer were similar to the results of other studies, apart from the primary prevention program that should be outlined according to prevalence of significant risk factors in the studied local community

  10. 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

    2015-01-01

    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.

  11. Anti-cancer agents based on 6-trifluoromethoxybenzimidazole derivatives and method of making

    Science.gov (United States)

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

    2012-10-23

    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.

  12. Laparoscopic ultrasonography--a method for staging of upper gastrointestinal cancer

    DEFF Research Database (Denmark)

    Durup Scheel-Hincke, J; Mortensen, M B; Pless, T;

    1999-01-01

    Laparoscopic ultrasonography (LUS) is a method that can be useful in the staging of upper gastrointestinal cancer. Dedicated transducers are available, and preliminary studies have proposed indications for the use of LUS staging of hepatic, esophageal, gastric, and pancreatic cancer disease. In the...

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

    OpenAIRE

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

    2012-01-01

    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.

  14. Digital Forensics Analysis of Spectral Estimation Methods

    CERN Document Server

    Mataracioglu, Tolga

    2011-01-01

    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.

  15. New Methods to Screen for Cancer Drugs and to Evaluate their Mechanism of Action

    OpenAIRE

    Rickardson, Linda

    2008-01-01

    Cancer is a common disease and due to problems with resistance against cancer drugs and the limited benefit from chemotherapy in many diagnoses, there is a need to develop new cancer drugs. In this thesis new methods to screen for cancer drugs and to evaluate their mechanism of action are discussed. In Paper I, it was found that by studying the gene expression of a cell line panel and combining the data with sensitivity data of a number of cytotoxic drugs, it was possible to cluster compounds...

  16. 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

    2011-01-01

    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.

  17. Thin-walled Cystic Lung Cancer: An Analysis of 24 Cases and Review of Literatures

    Directory of Open Access Journals (Sweden)

    Juntang GUO

    2014-07-01

    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.

  18. Sub-Thz Vibrational Spectroscopy for Analysis of Ovarian Cancer Cells

    Science.gov (United States)

    Ferrance, Jerome P.; Sizov, Igor; Jazaeri, Amir; Moyer, Aaron; Gelmont, Boris; Globus, Tatiana

    2016-06-01

    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.

  19. Computational methods for nuclear criticality safety analysis

    International Nuclear Information System (INIS)

    Nuclear criticality safety analyses require the utilization of methods which have been tested and verified against benchmarks results. In this work, criticality calculations based on the KENO-IV and MCNP codes are studied aiming the qualification of these methods at the IPEN-CNEN/SP and COPESP. The utilization of variance reduction techniques is important to reduce the computer execution time, and several of them are analysed. As practical example of the above methods, a criticality safety analysis for the storage tubes for irradiated fuel elements from the IEA-R1 research has been carried out. This analysis showed that the MCNP code is more adequate for problems with complex geometries, and the KENO-IV code shows conservative results when it is not used the generalized geometry option. (author)

  20. Heteroscedastic regression analysis method for mixed data

    Institute of Scientific and Technical Information of China (English)

    FU Hui-min; YUE Xiao-rui

    2011-01-01

    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.

  1. ORAL CONTRACEPTIVES AS A RISK FACTOR FOR DEVELOPING BREAST CANCER IN BREAST CANCER (BRCA) GENE CARRIER FEMALE IN- THE 30-60 YEARS AGE GROUP: A META-ANALYSIS

    OpenAIRE

    Ghimire S, Shrestha N, BK Baral

    2015-01-01

    The literature linking breast cancer with oral contraceptives and BRCA mutation as possible risk factors is equivocal. Hence, to account for these conflicting results in the existing literature and to observe the net effect, this meta-analysis aims to investigate whether oral contraceptives are a risk factor for developing breast cancer in breast cancer (BRCA) gene carrier female in the 30-60 years age group. Method: Systematic review of the literature, both published and unpublished, and met...

  2. Cancer research in need of a scientific revolution: Using 'paradigm shift' as a method of investigation.

    Science.gov (United States)

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

    2015-09-01

    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.

  3. Computer-aided methods for evaluating cancer risk in miners due to radiation exposure

    International Nuclear Information System (INIS)

    The paper presents some aspects of radiation hazard which occurs in a non-nuclear sector of industry, namely radiation hazard in non-uranium underground mines. The radiation hazard is caused in each type of underground mine by the naturally occurring noble radioactive gas-radon (222Rn) and radioactive products of its decay 218Po, 214Pb, 214Bi/214Po the so-called 'radon daughters' occurring in the mines' air. The paper presents the concept of how to provide a reliable system of assessment of miners' exposure by application of representative individual dosimetry, and also presents principles of computer-aided methods for interpretation of the results of miner's dosimetry useful for conversion of dosimetry data to the term of expected risk of cancer caused by exposure at miner's workplaces. The representative Individual Dosimetry system strengthened by computer-aided methods of analysis of results provided essential information on radiation cancer risk for miners employed in coal mines, metal-ore mines, chemical raw material mines in Poland. The coefficient of annual cancer risk induction is 1.5 x 10-4 year-1 for coal mines, 1.40 x 10-4 year-1 for metal ore mines and 1.5 x 10-4 year-1 for chemical raw material mines. The radiation risk appears to be of the same magnitude as the conventional risk of life loss at work-related accidents. The average Lost Life Expectancy coefficient for both the radiation risk and conventional risk are 0.5 and 0.3 year per each miner, respectively. (author)

  4. Computer-aided methods for evaluating cancer risk in miners due to radiation exposure.

    Science.gov (United States)

    Domański, T; Kluszczyński, D; Chruścielewski, W; Olszewski, J

    1993-01-01

    The paper presents some aspects of radiation hazard which occurs in a non-nuclear sector of industry, namely radiation hazard in non-uranium underground mines. The radiation hazard is caused in each type of underground mine by the naturally occurring noble radioactive gas-radon (222Rn) and radioactive products of its decay 218Po, 214Pb, 214Bi/214Po the so-called 'radon daughters' occurring in the mines' air. The paper presents the concept of how to provide a reliable system of assessment of miners' exposure by application of representative individual dosimetry, and also presents principles of computer-aided methods for interpretation of the results of miner's dosimetry useful for conversion of dosimetry data to the term of expected risk of cancer caused by exposure at miner's workplaces. The representative Individual Dosimetry system strengthened by computer-aided methods of analysis of results provided essential information on radiation cancer risk for miners employed in coal mines, metal-ore mines, chemical raw material mines in Poland. The coefficient of annual cancer risk induction is 1.5 x 10(-4) year-1 for coal mines, 1.40 x 10(-4) year-1 for metal ore mines and 1.5 x 10(-4) year-1 for chemical raw material mines. The radiation risk appears to be of the same magnitude as the conventional risk of life loss at work-related accidents. The average Lost Life Expectancy coefficient for both the radiation risk and conventional risk are 0.5 and 0.3 year per each miner, respectively. PMID:8019199

  5. Abnormal COX2 Protein Expression May Be Correlated with Poor Prognosis in Oral Cancer: A Meta-Analysis

    OpenAIRE

    Zhi-Ming Wang; Jie Liu; Hong-Bo Liu; Ming Ye; Yu-Fei Zhang; Dong-Sheng Yang

    2014-01-01

    Background. The prognostic significance of COX2 for survival of patients with oral cancer remains controversial. Thus, the meta-analysis was performed in order to identify COX2 expression impact on prognosis of oral cancer. Method. Relevant literatures were searched using the following electronic databases without any language restrictions: Web of Science, the Cochrane Library Database, PubMed, EMBASE, CINAHL, and CBM. Version 12.0 STATA software (Stata Corporation, College Station, Texas, US...

  6. The safety and efficacy of the preoperative neoadjuvant chemotherapy for patients with cervical cancer: a systematic review and meta analysis

    OpenAIRE

    Du HE; Duan, Chunyan; Chen, Jun; Lai, Lin; Chen, Jiaquan; Chen, Dian

    2015-01-01

    Objective: To evaluate the safety and efficacy of the preoperative neoadjuvant chemotherapy for patients with cervical cancer. Methods: A systematic literature search was conducted using the PubMed, EMBASE and Cochrane databases. Studies comparing combined neoadjuvant chemotherapy treatment (NACT)/radical surgery treatment (RST) with RST alone in patients with cervical cancer were eligible for inclusion. Results: Eight studies were finally included in this meta analysis, involving a total of ...

  7. Clinical value of serum human epididymis protein 4 assay in the diagnosis of ovarian cancer: a meta-analysis

    OpenAIRE

    Yang Z; Wei C; Luo Z; Li L

    2013-01-01

    Zhijun Yang,* Chunyin Wei,* Zhaoqing Luo, Li Li Department of Gynecologic Oncology, Guangxi Medical University, Nanning, People’s Republic of China *These authors contributed equally to this work Objective: Human epididymis protein 4 (HE4) has been approved for diagnosing ovarian cancer. The goal of this meta-analysis was to evaluate the clinical value of the serum HE4 in the diagnosis of ovarian cancer. Methods: The PubMed and Embase databases were searched to identify suitable studies...

  8. Functional genomic analysis of drug sensitivity pathways to guide adjuvant strategies in breast cancer

    DEFF Research Database (Denmark)

    Swanton, Charles; Szallasi, Zoltan Imre; Brenton, James D.;

    2008-01-01

    ) as well as endocrine therapies such as tamoxifen. Given the limited power of microarray signatures to predict therapeutic response in associative studies of small clinical trial cohorts, the use of functional genomic data combined with expression or sequence analysis of genes and microRNAs implicated...... in drug response in human tumours may provide a more robust method to guide adjuvant treatment strategies in breast cancer that are transferable across different expression platforms and patient cohorts....

  9. 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

    2010-01-01

    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...

  10. Aspirin Use and Lung Cancer Risk: A Possible Relationship? Evidence from an Updated Meta-Analysis

    OpenAIRE

    Hai-yan Jiang; Tian-bao Huang; Lei Xu; Jing Yu; Yan Wu; Jiang Geng; Xu-dong Yao

    2015-01-01

    Background and Purpose Growing evidence has emerged and controversial results reported on possible relationship between aspirin use and lung cancer risk. We, therefore, conducted this updated and comprehensive meta-analysis to evaluate this issue, with focus on dose-risk and duration-risk relationships. Methods We searched electronic databases including PUBMED, EMBASE and Cochrane library to identify eligible studies. Relative risk (RR) and its 95% confidence interval (CI) were used for cohor...

  11. Correlation between smoking history and molecular pathways in sporadic colorectal cancer: a meta-analysis

    OpenAIRE

    Chen, Ke; Xia, Guanggai; Zhang, Changhua; Sun, Yunwei

    2015-01-01

    Background: Epidemiological studies have shown that smoking increases the risk for colorectal cancer (CRC). Evidence of the guiding significance of smoking history for molecular classification and molecular targeted anti-tumor therapy is not well established. Aims: To provide indirectly evidence, we conducted a systematic meta-analysis of association between smoking history and different molecular classification. Methods: We searched in multiple databases up to January 2014, and identified 27...

  12. Prognostic classification index in Iranian colorectal cancer patients: Survival tree analysis

    OpenAIRE

    Malehi, Amal Saki; Rahim, Fakher

    2016-01-01

    Aims: The aim of this study was to determine the prognostic index for separating homogenous subgroups in colorectal cancer (CRC) patients based on clinicopathological characteristics using survival tree analysis. Methods: The current study was conducted at the Research Center of Gastroenterology and Liver Disease, Shahid Beheshti Medical University in Tehran, between January 2004 and January 2009. A total of 739 patients who already have been diagnosed with CRC based on pathologic report were...

  13. Dietary Cadmium Intake and the Risk of Cancer: A Meta-Analysis

    OpenAIRE

    Young Ae Cho; Jeongseon Kim; Hae Dong Woo; Moonsu Kang

    2013-01-01

    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 th...

  14. Correlating transcriptional networks to breast cancer survival: a large-scale coexpression analysis.

    OpenAIRE

    O'Driscoll, Lorraine

    2013-01-01

    PUBLISHED Weighted gene coexpression network analysis (WGCNA) is a powerful 'guilt-by-association'-based method to extract coexpressed groups of genes from large heterogeneous messenger RNA expression data sets. We have utilized WGCNA to identify 11 coregulated gene clusters across 2342 breast cancer samples from 13 microarray-based gene expression studies. A number of these transcriptional modules were found to be correlated to clinicopathological variables (e.g. tumor grade), survival en...

  15. 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

    2011-01-01

    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.

  16. Clinical Omics Analysis of Colorectal Cancer Incorporating Copy Number Aberrations and Gene Expression Data

    Directory of Open Access Journals (Sweden)

    Tsuyoshi Yoshida

    2010-07-01

    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

  17. Power System Transient Stability Analysis through a Homotopy Analysis Method

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Shaobu; Du, Pengwei; Zhou, Ning

    2014-04-01

    As an important function of energy management systems (EMSs), online contingency analysis plays an important role in providing power system security warnings of instability. At present, N-1 contingency analysis still relies on time-consuming numerical integration. To save computational cost, the paper proposes a quasi-analytical method to evaluate transient stability through time domain periodic solutions’ frequency sensitivities against initial values. First, dynamic systems described in classical models are modified into damping free systems whose solutions are either periodic or expanded (non-convergent). Second, because the sensitivities experience sharp changes when periodic solutions vanish and turn into expanded solutions, transient stability is assessed using the sensitivity. Third, homotopy analysis is introduced to extract frequency information and evaluate the sensitivities only from initial values so that time consuming numerical integration is avoided. Finally, a simple case is presented to demonstrate application of the proposed method, and simulation results show that the proposed method is promising.

  18. Multi-class texture analysis in colorectal cancer histology

    OpenAIRE

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

    2016-01-01

    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 pu...

  19. MICA polymorphisms and cancer risk: a meta-analysis.

    Science.gov (United States)

    Ji, Mengyao; Wang, Jun; Yuan, Lei; Zhang, Yunting; Zhang, Jixiang; Dong, Weiguo; Peng, Xiulan

    2015-01-01

    The major histocompatibility complex class I chain-related gene A transmembrane (MICA-TM) polymorphism has been implicated in susceptibility to cancer. However, the results are inconsistent. The aim of this meta-analysis is to evaluate the association between the MICA-TM polymorphisms and cancer risk. All eligible case-control studies published up to August 20, 2014 were identified by searching PubMed, Web of Science, CNKI and Wanfang databases. The cancer risk associated with the MICA polymorphism was estimated for each study by odds ratios (OR) together with its 95% confidence interval (CI), respectively. 21 studies from 19 publications with 3620 cases and 4903 controls were included. Overall, no significant associations between the MICA-TM polymorphism and cancer risk were found (A4 allele: OR = 0.97, 95% CI: 0.88-1.07; A5 allele: OR = 0.91, 95% CI: 0.81-1.04; A5.1 allele: OR = 1.03, 95% CI: 0.89-1.18; A6 allele: OR = 1.05, 95% CI: 0.95-1.15; A9 allele: OR = 0.96, 95% CI: 0.80-1.14; A10 allele: OR = 0.88, 95% CI: 0.43-1.79; del: OR = 2.50, 95% CI: 0.73-8.58; A7 allele: OR = 0.93, 95% CI: 0.43-2.00). When stratified by ethnicity, similar results were observed among Asians; however, there were significant association in Caucasian population for A5 (OR = 0.77, 95% CI: 0.68-0.87) and A9 allele (OR = 0.75, 95% CI: 0.66-0.85). This meta-analysis suggests that the MICA-TM A5 and A9 alleles may be an important protective factor for cancer in Caucasian populations.

  20. 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

    2011-01-01

    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.

  1. 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

    2012-01-01

    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.

  2. Cluster analysis of Wisconsin Breast Cancer dataset using self-organizing maps.

    Science.gov (United States)

    Pantazi, Stefan; Kagolovsky, Yuri; Moehr, Jochen R

    2002-01-01

    This work deals with multidimensional data analysis, precisely cluster analysis applied to a very well known dataset, the Wisconsin Breast Cancer dataset. After the introduction of the topics of the paper the cluster analysis concept is shortly explained and different methods of cluster analysis are compared. Further, the Kohonen model of self-organizing maps is briefly described together with an example and with explanations of how the cluster analysis can be performed using the maps. After describing the data set and the methodology used for the analysis we present the findings using textual as well as visual descriptions and conclude that the approach is a useful complement for assessing multidimensional data and that this dataset has been overused for automated decision benchmarking purposes, without a thorough analysis of the data it contains. PMID:15460731

  3. 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

    2008-01-01

    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.

  4. 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.

  5. A DECOMPOSITION METHOD OF STRUCTURAL DECOMPOSITION ANALYSIS

    Institute of Scientific and Technical Information of China (English)

    LI Jinghua

    2005-01-01

    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.

  6. Clinical Analysis of Lung Cancer Patients Younger Than 30 Years

    Directory of Open Access Journals (Sweden)

    Guangjie HOU

    2011-05-01

    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.

  7. Generalized analysis method for neutron resonance transmission analysis

    International Nuclear Information System (INIS)

    Neutron resonance densitometry (NRD) is a non-destructive analysis method, which can be applied to quantify special nuclear materials (SNM) in small particle-like debris of melted fuel that are formed in severe accidents of nuclear reactors such as the Fukushima Daiichi nuclear power plants. NRD uses neutron resonance transmission analysis (NRTA) to quantify SNM and neutron resonance capture analysis (NRCA) to identify matrix materials and impurities. To apply NRD for the characterization of arbitrary-shaped thick materials, a generalized method for the analysis of NRTA data has been developed. The method has been applied on data resulting from transmission through thick samples with an irregular shape and an areal density of SNM up to 0.253 at/b (≈100 g/cm2). The investigation shows that NRD can be used to quantify SNM with a high accuracy not only in inhomogeneous samples made of particle-like debris but also in samples made of large rocks with an irregular shape by applying the generalized analysis method for NRTA. (author)

  8. Association analysis of a chemo-response signature identified within The Cancer Genome Atlas aimed at predicting genetic risk for chemo-response in ovarian cancer

    Science.gov (United States)

    Salinas, Erin A; Newtson, Andreea M; Leslie, Kimberly K; Gonzalez-Bosquet, Jesus

    2016-01-01

    Background: A gene signature associated with chemo-response in ovarian cancer was created through integration of biological data in The Cancer Genome Atlas (TCGA) and validated in five independent microarray experiments. Our study aimed to determine if single nucleotide polymorphisms (SNPs) within the 422-gene signature were associated with a genetic predisposition to platinum-based chemotherapy response in serous ovarian cancer. Methods: An association analysis between SNPs within the 422-gene signature and chemo-response in serous ovarian cancer was performed under the log-additive genetic model using the ‘SNPassoc’ package within the R environment (p<0.0001). Subsequent validation of statistically significant SNPs was done in the Ovarian Cancer Association Consortium (OCAC) database. Results: 19 SNPs were found to be associated with chemo-response with statistical significance. None of the SNPs found significant in TCGA were validated within OCAC for the outcome of interest, chemo-response. Conclusions: SNPs associated with chemo-response in ovarian cancer within TGCA database were not validated in a larger database of patients and controls from OCAC. New strategies integrating somatic and germline information may help to characterize genetic predictors for treatment response in ovarian cancer. PMID:27186327

  9. Express analysis of HER-2/neu status in breast cancer biopsy specimens.

    Science.gov (United States)

    Nechaev, I N; Knyazev, E N; Krainova, N A; Shkurnikov, M Yu

    2013-08-01

    Hyperexpression of HER-2/neu is found in tissues of 25-30% patients with primary breast cancer. Monotherapy with antitumor drug trastuzumab as second-third line therapy and its combination with cytostatics prolong the interval before disease progress and the overall survival of patients with metastatic HER-2/neu+ tumors. Trastuzumab is now prescribed after evaluation of HER-2/neu status by the immunohistochemical method and/or fluorescent in situ hybridization. We have developed a method for evaluating the HER-2/neu status of breast cancer biopsy specimens by real time reverse transcription PCR. Based on the analysis of published data, six candidate genes in the pericentromer region of chromosome 17 are selected for data normalization. Stability of these genes is verified on the cell model (MCF-7 and SK-BR-3) and on biopsy materials. The sensitivity and specificity of the method is evaluated on a collection of biopsy specimens. PMID:24143382

  10. Spectroscopic Chemical Analysis Methods and Apparatus

    Science.gov (United States)

    Hug, William F.; Reid, Ray D.

    2012-01-01

    This invention relates to non-contact spectroscopic methods and apparatus for performing chemical analysis and the ideal wavelengths and sources needed for this analysis. It employs deep ultraviolet (200- to 300-nm spectral range) electron-beam-pumped wide bandgap semiconductor lasers, incoherent wide bandgap semiconductor lightemitting devices, and hollow cathode metal ion lasers. Three achieved goals for this innovation are to reduce the size (under 20 L), reduce the weight [under 100 lb (.45 kg)], and reduce the power consumption (under 100 W). This method can be used in microscope or macroscope to provide measurement of Raman and/or native fluorescence emission spectra either by point-by-point measurement, or by global imaging of emissions within specific ultraviolet spectral bands. In other embodiments, the method can be used in analytical instruments such as capillary electrophoresis, capillary electro-chromatography, high-performance liquid chromatography, flow cytometry, and related instruments for detection and identification of unknown analytes using a combination of native fluorescence and/or Raman spectroscopic methods. This design provides an electron-beampumped semiconductor radiation-producing method, or source, that can emit at a wavelength (or wavelengths) below 300 nm, e.g. in the deep ultraviolet between about 200 and 300 nm, and more preferably less than 260 nm. In some variations, the method is to produce incoherent radiation, while in other implementations it produces laser radiation. In some variations, this object is achieved by using an AlGaN emission medium, while in other implementations a diamond emission medium may be used. This instrument irradiates a sample with deep UV radiation, and then uses an improved filter for separating wavelengths to be detected. This provides a multi-stage analysis of the sample. To avoid the difficulties related to producing deep UV semiconductor sources, a pumping approach has been developed that uses

  11. Model-based methods for linkage analysis.

    Science.gov (United States)

    Rice, John P; Saccone, Nancy L; Corbett, Jonathan

    2008-01-01

    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.

  12. Investigation and analysis of oncologists' knowledge of morphine usage in cancer pain treatment

    Directory of Open Access Journals (Sweden)

    Liu W

    2014-05-01

    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

  13. Spatial Analysis Methods of Road Traffic Collisions

    DEFF Research Database (Denmark)

    Loo, Becky P. Y.; Anderson, Tessa Kate

    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......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...

  14. ANALYSIS METHOD OF AUTOMATIC PLANETARY TRANSMISSION KINEMATICS

    Directory of Open Access Journals (Sweden)

    Józef DREWNIAK

    2014-06-01

    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.

  15. Text analysis devices, articles of manufacture, and text analysis methods

    Science.gov (United States)

    Turner, Alan E; Hetzler, Elizabeth G; Nakamura, Grant C

    2013-05-28

    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.

  16. PIXE analysis of cancer-afflicted human bladder

    Energy Technology Data Exchange (ETDEWEB)

    Raju, G.J. Naga; Sarita, P.; Kumar, M. Ravi [Department of Physics, Institute of Technology, GITAM University, Visakhapatnam (India); Reddy, S. Bhuloka [Swami Jnanananda Laboratories for Nuclear Research, Andhra University, Visakhapatnam (India)

    2013-07-01

    Full text: The proton induced x-ray emission (PIXE) technique was used for analysis of trace elements in small quantities of biological samples. Both the biological samples of normal and cancer-afflicted human bladder tissues were studied. The present experiment was performed using a 3 MV pelletron accelerator at the Institute of Physics in Bhubaneswar, India. A proton beam of 3 MeV energy was used to excite the samples. NIST SRM 1577b Bovine Liver Tissue was used as external standards for the determination of trace element concentration in the biological tissue samples. The elements CI, K, Ca, Ti, Cr, Mn, Fe, Ni, Cu, Zn, and Se were identified and their concentrations were estimated. The concentrations of Ti and Zn are lower (p < 0.005) and that of Cr, Mn, Fe, Ni, and Cu are significantly higher (p < 0.001) in cancerous tissues than that in normal tissues. The deficiency or excess of different trace elements observed in the cancer tissues relative to the normal tissues of bladder are correlated to the pathology of cancer. (author)

  17. PIXE analysis of cancer-afflicted human bladder

    International Nuclear Information System (INIS)

    Full text: The proton induced x-ray emission (PIXE) technique was used for analysis of trace elements in small quantities of biological samples. Both the biological samples of normal and cancer-afflicted human bladder tissues were studied. The present experiment was performed using a 3 MV pelletron accelerator at the Institute of Physics in Bhubaneswar, India. A proton beam of 3 MeV energy was used to excite the samples. NIST SRM 1577b Bovine Liver Tissue was used as external standards for the determination of trace element concentration in the biological tissue samples. The elements CI, K, Ca, Ti, Cr, Mn, Fe, Ni, Cu, Zn, and Se were identified and their concentrations were estimated. The concentrations of Ti and Zn are lower (p < 0.005) and that of Cr, Mn, Fe, Ni, and Cu are significantly higher (p < 0.001) in cancerous tissues than that in normal tissues. The deficiency or excess of different trace elements observed in the cancer tissues relative to the normal tissues of bladder are correlated to the pathology of cancer. (author)

  18. 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;

    2014-01-01

    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....

  19. Cloud Based Development Issues: A Methodical Analysis

    Directory of Open Access Journals (Sweden)

    Sukhpal Singh

    2012-11-01

    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.

    Science.gov (United States)

    Yu, Lei; Andriola, Angelo

    2010-08-15

    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. Association of Vitamin E Intake with Reduced Risk of Kidney Cancer: A Meta-Analysis of Observational Studies

    OpenAIRE

    Shen, Chongxing; Huang, Ying; Yi, Shanhong; Fang, Zhenqiang; Li, Longkun

    2015-01-01

    Background Several observational studies suggested that vitamin E intake is related to the risk of kidney cancer; however, the results of published studies are inconsistent. Material/Methods A meta-analysis was performed to assess the relationship between vitamin E intake and the risk of kidney cancer by searching PubMed and Medline through August 2015. We computed pooled relative risks (RR) and 95%CI of kidney cancer for the highest versus lowest level of vitamin E intake. Results A total of...

  2. Single-cell analysis - Methods and protocols

    Directory of Open Access Journals (Sweden)

    Carlo Alberto Redi

    2013-06-01

    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....

  3. Prioritizing therapeutics for lung cancer: an integrative meta-analysis of cancer gene signatures and chemogenomic data.

    Directory of Open Access Journals (Sweden)

    Kristen Fortney

    2015-03-01

    Full Text Available Repurposing FDA-approved drugs with the aid of gene signatures of disease can accelerate the development of new therapeutics. A major challenge to developing reliable drug predictions is heterogeneity. Different gene signatures of the same disease or drug treatment often show poor overlap across studies, as a consequence of both biological and technical variability, and this can affect the quality and reproducibility of computational drug predictions. Existing algorithms for signature-based drug repurposing use only individual signatures as input. But for many diseases, there are dozens of signatures in the public domain. Methods that exploit all available transcriptional knowledge on a disease should produce improved drug predictions. Here, we adapt an established meta-analysis framework to address the problem of drug repurposing using an ensemble of disease signatures. Our computational pipeline takes as input a collection of disease signatures, and outputs a list of drugs predicted to consistently reverse pathological gene changes. We apply our method to conduct the largest and most systematic repurposing study on lung cancer transcriptomes, using 21 signatures. We show that scaling up transcriptional knowledge significantly increases the reproducibility of top drug hits, from 44% to 78%. We extensively characterize drug hits in silico, demonstrating that they slow growth significantly in nine lung cancer cell lines from the NCI-60 collection, and identify CALM1 and PLA2G4A as promising drug targets for lung cancer. Our meta-analysis pipeline is general, and applicable to any disease context; it can be applied to improve the results of signature-based drug repurposing by leveraging the large number of disease signatures in the public domain.

  4. Analysis of Fiber deposition using Automatic Image Processing Method

    Science.gov (United States)

    Belka, M.; Lizal, F.; Jedelsky, J.; Jicha, M.

    2013-04-01

    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.

  5. Analysis of Fiber deposition using Automatic Image Processing Method

    Directory of Open Access Journals (Sweden)

    Jicha M.

    2013-04-01

    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.

  6. Finite Volume Methods: Foundation and Analysis

    Science.gov (United States)

    Barth, Timothy; Ohlberger, Mario

    2003-01-01

    Finite volume methods are a class of discretization schemes that have proven highly successful in approximating the solution of a wide variety of conservation law systems. They are extensively used in fluid mechanics, porous media flow, meteorology, electromagnetics, models of biological processes, semi-conductor device simulation and many other engineering areas governed by conservative systems that can be written in integral control volume form. This article reviews elements of the foundation and analysis of modern finite volume methods. The primary advantages of these methods are numerical robustness through the obtention of discrete maximum (minimum) principles, applicability on very general unstructured meshes, and the intrinsic local conservation properties of the resulting schemes. Throughout this article, specific attention is given to scalar nonlinear hyperbolic conservation laws and the development of high order accurate schemes for discretizing them. A key tool in the design and analysis of finite volume schemes suitable for non-oscillatory discontinuity capturing is discrete maximum principle analysis. A number of building blocks used in the development of numerical schemes possessing local discrete maximum principles are reviewed in one and several space dimensions, e.g. monotone fluxes, E-fluxes, TVD discretization, non-oscillatory reconstruction, slope limiters, positive coefficient schemes, etc. When available, theoretical results concerning a priori and a posteriori error estimates are given. Further advanced topics are then considered such as high order time integration, discretization of diffusion terms and the extension to systems of nonlinear conservation laws.

  7. Spectroscopic chemical analysis methods and apparatus

    Science.gov (United States)

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

    2013-01-01

    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. Chemical analysis instruments employed in some embodiments include capillary and gel plane electrophoresis, capillary electrochromatography, high performance liquid chromatography, flow cytometry, flow cells for liquids and aerosols, and surface detection 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.

  8. Contrast enhanced MR imaging of female pelvic cancers: Established methods and emerging applications

    Energy Technology Data Exchange (ETDEWEB)

    Punwani, Shonit, E-mail: shonit.punwani@gmail.com [Department of Academic Radiology, 2nd Floor Podium, University College London Hospital, 235 Euston Road, London NW1 2BU (United Kingdom)

    2011-04-15

    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.

  9. Spectral and structural studies of the anti-cancer drug Flutamide by density functional theoretical method

    Science.gov (United States)

    Mariappan, G.; Sundaraganesan, N.

    2014-01-01

    A comprehensive screening of the more recent DFT theoretical approach to structural analysis is presented in this section of theoretical structural analysis. The chemical name of 2-methyl-N-[4-nitro-3-(trifluoromethyl)phenyl]-propanamide is usually called as Flutamide (In the present study it is abbreviated as FLT) and is an important and efficacious drug in the treatment of anti-cancer resistant. The molecular geometry, vibrational spectra, electronic and NMR spectral interpretation of Flutamide have been studied with the aid of density functional theory method (DFT). The vibrational assignments of the normal modes were performed on the basis of the PED calculations using the VEDA 4 program. Comparison of computational results with X-ray diffraction results of Flutamide allowed the evaluation of structure predictions and confirmed B3LYP/6-31G(d,p) as accurate for structure determination. Application of scaling factors for IR and Raman frequency predictions showed good agreement with experimental values. This is supported the assignment of the major contributors of the vibration modes of the title compound. Stability of the molecule arising from hyperconjugative interactions leading to its bioactivity, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. NMR chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. The comparison of measured FTIR, FT-Raman, and UV-Visible data to calculated values allowed assignment of major spectral features of the title molecule. Besides, Frontier molecular orbital analyze was also investigated using theoretical calculations.

  10. Meta-Analysis of a Multi-Ethnic, Breast Cancer Case-Control Targeted Sequencing Study

    OpenAIRE

    Ablorh, Akweley

    2015-01-01

    Breast cancer, the most commonly diagnosed cancer in American women, is a heritable disease with nearly one hundred known genetic risk factors. Using next generation sequencing, we explored the contribution of genetics at 12 GWAS-identified loci to breast cancer susceptibility in a multi-ethnic breast cancer case-control study. Methods: The study population consists of 4,611 breast cancer cases and controls (2,316 cases and 2,295 controls) from four mutually exclusive ethnicities: Africa...

  11. Statistical trend analysis methods for temporal phenomena

    International Nuclear Information System (INIS)

    We consider point events occurring in a random way in time. In many applications the pattern of occurrence is of intrinsic interest as indicating a trend or some other systematic feature in the rate of occurrence. The purpose of this report is to survey briefly different statistical trend analysis methods and illustrate their applicability to temporal phenomena in particular. The trend testing of point events is usually seen as the testing of the hypotheses concerning the intensity of the occurrence of events. When the intensity function is parametrized, the testing of trend is a typical parametric testing problem. In industrial applications the operational experience generally does not suggest any specified model and method in advance. Therefore, and particularly, if the Poisson process assumption is very questionable, it is desirable to apply tests that are valid for a wide variety of possible processes. The alternative approach for trend testing is to use some non-parametric procedure. In this report we have presented four non-parametric tests: The Cox-Stuart test, the Wilcoxon signed ranks test, the Mann test, and the exponential ordered scores test. In addition to the classical parametric and non-parametric approaches we have also considered the Bayesian trend analysis. First we discuss a Bayesian model, which is based on a power law intensity model. The Bayesian statistical inferences are based on the analysis of the posterior distribution of the trend parameters, and the probability of trend is immediately seen from these distributions. We applied some of the methods discussed in an example case. It should be noted, that this report is a feasibility study rather than a scientific evaluation of statistical methods, and the examples can only be seen as demonstrations of the methods

  12. Chemotherapy versus support cancer treatment in advanced gastric cancer: a meta-analysis

    Directory of Open Access Journals (Sweden)

    L. Casaretto

    2006-04-01

    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.

  13. 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

    2004-01-01

    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.

  14. Survival analysis of colorectal cancer patients with tumor recurrence using global score test methodology

    International Nuclear Information System (INIS)

    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

  15. Analysis of variabilities of serum proteomic spectra in patients with gastric cancer before and after operation

    Institute of Scientific and Technical Information of China (English)

    Hong Ren; Ning Du; Gang Liu; Heng-Tong Hu; Wei Tian; Zhi-Ping Deng; Jing-Sen Shi

    2006-01-01

    AIM: To study the variabilities of serum proteomic spectra in patients with gastric cancer before and after operation in order to detect the specific protein markers that can be used for quick diagnosis of gastric cancer.METHODS: Proteomic spectra of 46 serum samples from patients with gastric cancer before and after operation and 40 from normal individuals were generated by IMAC-Cu protein chip and surface-enhanced laser desorption/ionization time of flight mass spectrometry.RESULTS: Fourteen differentially expressed proteins in serum were screened by analysis of proteomic spectra of preoperative patients and normal individuals. We obtained 4 proteins (heat shock protein 27, glucoseregulated protein, prohibitin, protein disulfide isomerase A3) making up marker pattern which was able to class the patient-team and normal-team. These marker patterns yielded 95.7% sensitivity and 92.5% specificity,respectively. The proteins over-expressed in serum of preoperative patients were obviously down-regulated.CONCLUSION: Specific protein markers of gastric cancer can be used for the quick diagnosis of gastric cancer and judgment of prognosis. SELDI-TOF-MS is a useful tool for the detection and identification of new protein markers in serum.

  16. Survival analysis of colorectal cancer patients with tumor recurrence using global score test methodology

    Science.gov (United States)

    Zain, Zakiyah; Aziz, Nazrina; Ahmad, Yuhaniz; Azwan, Zairul; Raduan, Farhana; Sagap, Ismail

    2014-12-01

    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.

  17. Risk-benefit analysis for mass screening of breast cancer utilizing mammography as a screening test

    International Nuclear Information System (INIS)

    Incidence of breast cancers in Japanese women is increasing steadily. Mass screening of breast cancer was started in Japan under auspices of Adult Health Promotion Act of the Japanese Government from 1987. As the first screening method, the palpation of breasts is employed at present, but it is expected to be replaced by the mammography. In this report, the risk-benefit analysis is presented between risk of breast carcinogenesis due to radiation and benefit of mass screening of breast cancer. The benefit of mass screening is taken as the net elongation of average life expectancy of women due to survival from breast cancers. The risk of mammography is taken as the net loss of average life expectancy of women due to breast carcinogenesis. In the latter, the latency time and plateau period of radiation carcinogenesis were taken into consideration in the calculation. The results show that the ages at which the benefit and risk become equal are between 30 and 35 years old when dose equivalent of mammography is between 10 and 20 mSv, that are conventionally used. However, the critical age will be reduced to 20 years old if the dose equivalent becomes 1 mSv. Therefore, it is strongly recommended that a low dose mammographic system should be developed in order to achieve 1 mSv for the mass screening of breast cancer of Japanese women. In author's opinion, this is quite feasible by employing a new digital radiography with imaging plate. (author)

  18. Survival analysis of colorectal cancer patients with tumor recurrence using global score test methodology

    Energy Technology Data Exchange (ETDEWEB)

    Zain, Zakiyah, E-mail: zac@uum.edu.my; Ahmad, Yuhaniz, E-mail: yuhaniz@uum.edu.my [School of Quantitative Sciences, Universiti Utara Malaysia, UUM Sintok 06010, Kedah (Malaysia); Azwan, Zairul, E-mail: zairulazwan@gmail.com, E-mail: farhanaraduan@gmail.com, E-mail: drisagap@yahoo.com; Raduan, Farhana, E-mail: zairulazwan@gmail.com, E-mail: farhanaraduan@gmail.com, E-mail: drisagap@yahoo.com; Sagap, Ismail, E-mail: zairulazwan@gmail.com, E-mail: farhanaraduan@gmail.com, E-mail: drisagap@yahoo.com [Surgery Department, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, 56000 Bandar Tun Razak, Kuala Lumpur (Malaysia); Aziz, Nazrina, E-mail: nazrina@uum.edu.my

    2014-12-04

    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.

  19. Preventing aggressive prostate cancer with proven cardiovascular disease preventive methods

    OpenAIRE

    Moyad, Mark A

    2015-01-01

    Cardiovascular disease (CVD) has been the number one cause of death in the U.S. for 114 of the last 115 years. Risk factors for prostate cancer have primarily mirrored risk proven risk factors for CVD, especially aggressive disease. Obesity, dyslipidemia, glucose intolerance, metabolic syndrome, unhealthy dietary habits or caloric excess, lack of physical activity, and inflammation are just some of these shared risk factors. The evidence also suggests proven CVD preventive measures are identi...

  20. Impact of the Choice of Normalization Method on Molecular Cancer Class Discovery Using Nonnegative Matrix Factorization

    Science.gov (United States)

    Yang, Haixuan; Seoighe, Cathal

    2016-01-01

    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: http://maths.nuigalway.ie/~haixuanyang/pNMF/pNMF.htm. PMID:27741311

  1. Association between dietary vitamin C intake and risk of esophageal cancer: A dose-response meta-analysis.

    Science.gov (United States)

    Bo, Yacong; Lu, Yan; Zhao, Yan; Zhao, Erjiang; Yuan, Ling; Lu, Weiquan; Cui, Lingling; Lu, Quanjun

    2016-04-15

    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.

  2. 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

    2011-01-01

    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.

  3. 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

    2013-10-01

    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

  4. Data Analysis Methods for Library Marketing

    Science.gov (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.

  5. Review of Computational Stirling Analysis Methods

    Science.gov (United States)

    Dyson, Rodger W.; Wilson, Scott D.; Tew, Roy C.

    2004-01-01

    Nuclear thermal to electric power conversion carries the promise of longer duration missions and higher scientific data transmission rates back to Earth for both Mars rovers and deep space missions. A free-piston Stirling convertor is a candidate technology that is considered an efficient and reliable power conversion device for such purposes. While already very efficient, it is believed that better Stirling engines can be developed if the losses inherent its current designs could be better understood. However, they are difficult to instrument and so efforts are underway to simulate a complete Stirling engine numerically. This has only recently been attempted and a review of the methods leading up to and including such computational analysis is presented. And finally it is proposed that the quality and depth of Stirling loss understanding may be improved by utilizing the higher fidelity and efficiency of recently developed numerical methods. One such method, the Ultra HI-Fl technique is presented in detail.

  6. Analysis and estimation of risk management methods

    Directory of Open Access Journals (Sweden)

    Kankhva Vadim Sergeevich

    2016-05-01

    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.

  7. Optical methods for the analysis of dermatopharmacokinetics

    Science.gov (United States)

    Lademann, Juergen; Weigmann, Hans-Juergen; von Pelchrzim, R.; Sterry, Wolfram

    2002-07-01

    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.

  8. Lung cancer associated hypercalcemia: An analysis of factors influencing survival and prognosis in 34 cases

    Directory of Open Access Journals (Sweden)

    Su-jie ZHANG

    2012-06-01

    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.

  9. ANALYSIS OF RELAPSE RATE AND METASTASES OF HIGH DIFFERENTIATED THYROID CANCER

    Directory of Open Access Journals (Sweden)

    E. V. Savenok

    2015-01-01

    Full Text Available  Analysis of rate of relapses and metastases with well-differentiated thyroid cancer was performed for patients in 2009 to 2013. The study involved 189 patients with thyroid cancer including 98 (51.9 % patients suffering from papillary thyroid cancer, 77 (40.7 % patients suffering from follicular thyroid cancer, and 14 (7.4 % patients suffering from medullary thyroid cancer. 2.04 % of the 98 patients suffering from papillary thyroid cancer manifested a relapse, and lymphogenic metastases of cancer were revealed with 1.0 % of patients. With follicular thyroid cancer (n = 77, lymphogenic metastases were registered in 7.8 % of cases, relapses were revealed in 1.3 % of cases. This analysis demonstrated that observation of patients for 5 years revealed a higher percentage of metastases with patients that suffered from follicular thyroid cancer.

  10. Identification of Personalized Chemoresistance Genes in Subtypes of Basal-Like Breast Cancer Based on Functional Differences Using Pathway Analysis.

    Directory of Open Access Journals (Sweden)

    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

  11. Diagnostic accuracy of circulating tumor cells detection in gastric cancer: systematic review and meta-analysis

    International Nuclear Information System (INIS)

    Circulating tumor cells (CTCs) detection has previously been used for diagnosing gastric cancer. However, the previous studies failed to make an agreement whether the detection of CTCs contributes to the diagnosis of gastric cancer. A systematic review and meta-analysis was performed to evaluate the overall accuracy of CTCs detection for diagnosing gastric cancer. PubMed, Embase and the Wanfang database were searched in all languages published up to Oct 2012. The pooled sensitivity (SEN), specificity (SPE), positive and negative likelihood ratios (PLR and NLR, respectively), diagnostic odds ratio (DOR) and summary receiver operating characteristic (sROC) curve were calculated to evaluate the overall test performance. Twenty studies were included in this systematic review and meta-analysis. The diagnostic value of CTCs detection for the gastric cancer was calculated to evaluate the overall test performance. The summary estimates of The pooled sensitivity, specificity, positive and negative likelihood ratios, diagnostic odds ratio were 0.42 (95% confidence interval (CI), 0.21-0.67), 0.99 (95% CI, 0.96-1.00), 58.2 (95% CI, 9.8-345.9), 0.58 (95% CI, 0.38-0.89), and 100 (95% CI, 15–663), respectively. The summary receiver operating characteristic curve was 0.97 (95% CI, 0.95–0.98). Deek’s funnel plot asymmetry test found no evidence of study publication bias in the current study (P = 0.49). This systematic review suggests that CTCs detection alone cannot be recommended as a screening test for gastric cancer. However, it might be used as a noninvasive method for the confirmation of the gastric cancer diagnosis

  12. Geostatistical Analysis of County-Level Lung Cancer Mortality Rates in the Southeastern United States.

    Science.gov (United States)

    Goovaerts, Pierre

    2010-01-01

    The analysis of health data and putative covariates, such as environmental, socioeconomic, demographic, behavioral, or occupational factors, is a promising application for geostatistics. Transferring methods originally developed for the analysis of earth properties to health science, however, presents several methodological and technical challenges. These arise because health data are typically aggregated over irregular spatial supports (e.g., counties) and consist of a numerator and a denominator (i.e., rates). This article provides an overview of geostatistical methods tailored specifically to the characteristics of areal health data, with an application to lung cancer mortality rates in 688 U.S. counties of the southeast (1970-1994). Factorial Poisson kriging can filter short-scale variation and noise, which can be large in sparsely populated counties, to reveal similar regional patterns for male and female cancer mortality that correlate well with proximity to shipyards. Rate uncertainty was transferred through local cluster analysis using stochastic simulation, allowing the computation of the likelihood of clusters of low or high cancer mortality. Accounting for population size and rate uncertainty led to the detection of new clusters of high mortality around Oak Ridge National Laboratory for both sexes, in counties with high concentrations of pig farms and paper mill industries for males (occupational exposure) and in the vicinity of Atlanta for females. PMID:20445829

  13. 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.

  14. Pathway analysis of genome-wide association study data highlights pancreatic development genes as susceptibility factors for pancreatic cancer

    OpenAIRE

    Li, Donghui; Duell, Eric J.; Yu, Kai; Risch, Harvey A.; Olson, Sara H.; Kooperberg, Charles; Wolpin, Brian M.; Jiao, Li; Dong, Xiaoqun; Wheeler, Bill; Arslan, Alan A.; Bueno-De-Mesquita, H Bas; Fuchs, Charles S; Gallinger, Steven; Gross, Myron

    2012-01-01

    Four loci have been associated with pancreatic cancer through genome-wide association studies (GWAS). Pathway-based analysis of GWAS data is a complementary approach to identify groups of genes or biological pathways enriched with disease-associated single-nucleotide polymorphisms (SNPs) whose individual effect sizes may be too small to be detected by standard single-locus methods. We used the adaptive rank truncated product method in a pathway-based analysis of GWAS data from 3851 pancreatic...

  15. Analysis of primary risk factors for oral cancer from select US states with increasing rates

    Directory of Open Access Journals (Sweden)

    O'Malley Susan

    2010-02-01

    Full Text Available Abstract Objectives To examine the primary risk factor for oral cancer in the US, smoking and tobacco use, among the specific US states that experienced short-term increases in oral cancer incidence and mortality. Methods Population-based data on oral cancer morbidity and mortality in the US were obtained from the National Cancer Institute's (NCI Surveillance, Epidemiology, and End Results (SEER database for analysis of recent trends. Data were also obtained from the Centers for Disease Control and Prevention (CDC Behavioral Risk Factor Surveillance System (BRFSS to measure current and former trends of tobacco usage. To comprehensive measures of previous state tobacco use and tobacco-related policies, the Initial Outcomes Index (IOI, 1992-1993 and the Strength of Tobacco Control index (SoTC, 1999-2000 were also used for evaluation and comparison. Results Analysis of the NCI-SEER data confirmed a previous report of geographic increases in oral cancer and demonstrated these were state-specific, were not regional, and were unrelated to previously observed increases among females and minorities. Analysis of the CDC-BRFSS data revealed these states had relatively higher percentages of smokers currently, as well as historically. In addition, analysis of the IOI and SoTC indexes suggest that many factors, including cigarette pricing, taxes and home or workplace bans, may have had significant influence on smoking prevalence in these areas. Trend analysis of these data uncovered a recent and significant reversal in smoking rates that suggest oral cancer incidence and mortality may also begin to decline in the near future. Conclusion Due to the rising costs of health care in the US and the limited resources available for health prevention efforts, it is essential to organize and direct more effective efforts by public health officials and epidemiologists, as well as funding from local, state and federal governments, to reduce and eliminate identified

  16. New Breast Cancer Recursive Partitioning Analysis Prognostic Index in Patients With Newly Diagnosed Brain Metastases

    International Nuclear Information System (INIS)

    Purpose: The aim of the study was to present a new breast cancer recursive partitioning analysis (RPA) prognostic index for patients with newly diagnosed brain metastases as a guide in clinical decision making. Methods and Materials: A prospectively collected group of 441 consecutive patients with breast cancer and brain metastases treated between the years 2003 and 2009 was assessed. Prognostic factors significant for univariate analysis were included into RPA. Results: Three prognostic classes of a new breast cancer RPA prognostic index were selected. The median survival of patients within prognostic Classes I, II, and III was 29, 9, and 2.4 months, respectively (p < 0.0001). Class I included patients with one or two brain metastases, without extracranial disease or with controlled extracranial disease, and with Karnofsky performance status (KPS) of 100. Class III included patients with multiple brain metastases with KPS of ≤60. Class II included all other cases. Conclusions: The breast cancer RPA prognostic index is an easy and valuable tool for use in clinical practice. It can select patients who require aggressive treatment and those in whom whole-brain radiotherapy or symptomatic therapy is the most reasonable option. An individual approach is required for patients from prognostic Class II.

  17. The benchmark analysis of gastric, colorectal and rectal cancer pathways: toward establishing standardized clinical pathway in the cancer care.

    Science.gov (United States)

    Ryu, Munemasa; Hamano, Masaaki; Nakagawara, Akira; Shinoda, Masayuki; Shimizu, Hideaki; Miura, Takeshi; Yoshida, Isao; Nemoto, Atsushi; Yoshikawa, Aki

    2011-01-01

    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.

  18. Effects of manual lymphatic drainage on breast cancer-related lymphedema: a systematic review and meta-analysis of randomized controlled trials

    OpenAIRE

    Huang Tsai-Wei; Tseng Sung-Hui; Lin Chia-Chin; Bai Chyi-Huey; Chen Ching-Shyang; Hung Chin-Sheng; Wu Chih-Hsiung; Tam Ka-Wai

    2013-01-01

    Abstract Background Lymphedema is a common complication of axillary dissection for breast cancer. We investigated whether manual lymphatic drainage (MLD) could prevent or manage limb edema in women after breast-cancer surgery. Methods We performed a systematic review and meta-analysis of published randomized controlled trials (RCTs) to evaluate the effectiveness of MLD in the prevention and treatment of breast-cancer-related lymphedema. The PubMed, EMBASE, CINAHL, Physiotherapy Evidence Datab...

  19. Chemotherapy-associated thromboembolic risk in cancer outpatients and effect of nadroparin thromboprophylaxis: results of a retrospective analysis of the PROTECHT study

    OpenAIRE

    Petrelli Fausto; Brighenti Matteo; Mandalà Mario; Verso Melina; Bonizzoni Erminio; Agnelli Giancarlo; Labianca Roberto; Barni Sandro; Bianchini Carlo; Perrone Tania; Gasparini Giampietro

    2011-01-01

    Abstract Background Cancer patients receiving chemotherapy are at increased risk of thrombosis. Nadroparin has been demonstrated to reduce the incidence of venous and arterial thrombotic events (TEs) by about 50% in cancer outpatients receiving chemotherapy. The aims of this retrospective analysis were to evaluate the thromboembolic risk and the benefit of thromboprophylaxis according to type of chemotherapy. Methods Cancer outpatients were randomly assigned to receive subcutaneous injections...

  20. Impact of BCL2 and p53 on postmastectomy radiotherapy response in high-risk breast cancer. A subgroup analysis of DBCG82 b&c

    DEFF Research Database (Denmark)

    Kyndi, Marianne; Sørensen, Flemming Brandt; Knudsen, Helle;

    2008-01-01

    PURPOSE: To examine p53 and BCL2 expression in high-risk breast cancer patients randomized to postmastectomy radiotherapy (PMRT). PATIENTS AND METHODS: The present analysis included 1 000 of 3 083 high-risk breast cancer patients randomly assigned to PMRT in the DBCG82 b&c studies. Tissue microar...

  1. 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

    2013-01-01

    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。

  2. 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

    2011-01-01

    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

  3. 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;

    2015-01-01

    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...

  4. Who Benefits From Adjuvant Radiation Therapy for Gastric Cancer? A Meta-Analysis

    International Nuclear Information System (INIS)

    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

  5. 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.

    OpenAIRE

    Paone, G; De Angelis, G.; Portalone, L.; Greco, S.; Giosué, S.; Taglienti, A.; Bisetti, A; Ameglio, F.

    1997-01-01

    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...

  6. Thermal Analysis Methods for Aerobraking Heating

    Science.gov (United States)

    Amundsen, Ruth M.; Gasbarre, Joseph F.; Dec, John A.

    2005-01-01

    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

  7. Blood proteins analysis by Raman spectroscopy method

    Science.gov (United States)

    Artemyev, D. N.; Bratchenko, I. A.; Khristoforova, Yu. A.; Lykina, A. A.; Myakinin, O. O.; Kuzmina, T. P.; Davydkin, I. L.; Zakharov, V. P.

    2016-04-01

    This work is devoted to study the possibility of plasma proteins (albumin, globulins) concentration measurement using Raman spectroscopy setup. The blood plasma and whole blood were studied in this research. The obtained Raman spectra showed significant variation of intensities of certain spectral bands 940, 1005, 1330, 1450 and 1650 cm-1 for different protein fractions. Partial least squares regression analysis was used for determination of correlation coefficients. We have shown that the proposed method represents the structure and biochemical composition of major blood proteins.

  8. Semiquantitative fluorescence method for bioconjugation analysis.

    Science.gov (United States)

    Brasil, Aluízio G; Carvalho, Kilmara H G; Leite, Elisa S; Fontes, Adriana; Santos, Beate Saegesser

    2014-01-01

    Quantum dots (QDs) have been used as fluorescent probes in biological and medical fields such as bioimaging, bioanalytical, and immunofluorescence assays. For these applications, it is important to characterize the QD-protein bioconjugates. This chapter provides details on a versatile method to confirm quantum dot-protein conjugation including the required materials and instrumentation in order to perform the step-by-step semiquantitative analysis of the bioconjugation efficiency by using fluorescence plate readings. Although the protocols to confirm the QD-protein attachment shown here were developed for CdTe QDs coated with specific ligands and proteins, the principles are the same for other QDs-protein bioconjugates. PMID:25103803

  9. Method and apparatus for simultaneous spectroelectrochemical analysis

    Science.gov (United States)

    Chatterjee, Sayandev; Bryan, Samuel A; Schroll, Cynthia A; Heineman, William R

    2013-11-19

    An apparatus and method of simultaneous spectroelectrochemical analysis is disclosed. A transparent surface is provided. An analyte solution on the transparent surface is contacted with a working electrode and at least one other electrode. Light from a light source is focused on either a surface of the working electrode or the analyte solution. The light reflected from either the surface of the working electrode or the analyte solution is detected. The potential of the working electrode is adjusted, and spectroscopic changes of the analyte solution that occur with changes in thermodynamic potentials are monitored.

  10. Cannabis Smoking and Risk of Lung Cancer - A Systematic Review and Meta-Analysis

    Directory of Open Access Journals (Sweden)

    khalid BOUTI

    2014-12-01

    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.

  11. A meta-analysis of bevacizumab combined with chemotherapy in the treatment of ovarian cancer

    Directory of Open Access Journals (Sweden)

    T S Wang

    2014-01-01

    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 (http://www.stata.com; 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

  12. FUZZY METHOD FOR FAILURE CRITICALITY ANALYSIS

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    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.

  13. 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

    2005-01-01

    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.

  14. Relationship Between Murine Double Minute 2 (MDM2) T309G Polymorphism and Endometrial Cancer Risk: A Meta-Analysis.

    Science.gov (United States)

    Xue, Zhuowei; Zhu, Xiaolu; Teng, Yincheng

    2016-01-01

    BACKGROUND Endometrial cancer is one of the most common cancers in female patients. Many studies have investigated the association between the MDM2 T309G genotype and endometrial cancer incidence, but the results have been inconclusive. MATERIAL AND METHODS We performed a systematic search in PubMed and Web of Science databases (update until October 21, 2015) for all English-language publications. The associations are indicated as pooled odds ratio (OR) and 95% confidence intervals (CI). RESULTS We identified 8 relevant publications (9 case-control studies), including 2188 cases and 4654 controls, that assessed the relationship between MDM2 T309G polymorphism and endometrial cancer risk. There was a significant association between MDM2 T309G polymorphism and endometrial cancer risk in the overall population in the recessive model (OR=1.61; 95% CI: 1.19-2.19; P=0.002). In the subgroup of different ethnic populations, the subgroup analysis showed MDM2 T309G polymorphism was significantly associated with increased endometrial cancer risk in Caucasians (OR=1.75; 95% CI: 1.16-2.63; P=0.007). No similar result was found in Asians. CONCLUSIONS Our meta-analysis provides evidence that MDM2 T309G polymorphism is associated with endometrial cancer, especially in Caucasians. PMID:27604213

  15. 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

    2009-12-01

    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

  16. Immunohistochemical analysis of Metadherin in proliferative and cancerous breast tissue

    OpenAIRE

    Zhang Qinghui; Su Peng; Yang Qifeng

    2010-01-01

    Abstract Background Metadherin (MTDH) has been reported to be associated with cancer progression in various types of human cancers including breast cancer. Whether MTDH contributes to carcinogenesis of breast cancer is still unknown. In the present study, we investigated the expression of MTDH in normal, UDH (usual ductal hyperplasia), ADH (atypical ductal hyperplasia), DCIS (ductal carcinoma in situ) and invasive cancer to explore the possible role of MTDH for breast cancer carcinogenesis. M...

  17. Label-Free Quantitative Proteomics and N-terminal Analysis of Human Metastatic Lung Cancer Cells

    OpenAIRE

    Min, Hophil; Han, Dohyun; Kim, Yikwon; Cho, Jee Yeon; Jin, Jonghwa; Kim, Youngsoo

    2014-01-01

    Proteomic analysis is helpful in identifying cancer-associated proteins that are differentially expressed and fragmented that can be annotated as dysregulated networks and pathways during metastasis. To examine meta-static process in lung cancer, we performed a proteomics study by label-free quantitative analysis and N-terminal analysis in 2 human non-small-cell lung cancer cell lines with disparate metastatic potentials—NCI-H1703 (primary cell, stage I) and NCI-H1755 (metastatic cell, stage ...

  18. Integrated Analysis of Germline and Somatic Variants in Ovarian Cancer

    OpenAIRE

    Kanchi, Krishna L.; Johnson, Kimberly J.; Lu, Charles; McLellan, Michael D; Mark D M Leiserson; Wendl, Michael C; Zhang, Qunyuan; Koboldt, Daniel C.; Xie, Mingchao; Kandoth, Cyriac; McMichael, Joshua F.; Wyczalkowski, Matthew A.; Larson, David E.; Schmidt, Heather K.; Christopher A Miller

    2014-01-01

    We report the first large-scale exome-wide analysis of the combined germline-somatic landscape in ovarian cancer. Here we analyze germline and somatic alterations in 429 ovarian carcinoma cases and 557 controls. We identify 3,635 high confidence, rare truncation and 22,953 missense variants with predicted functional impact. We find germline truncation variants and large deletions across Fanconi pathway genes in 20% of cases. Enrichment of rare truncations is shown in BRCA1, BRCA2, and PALB2. ...

  19. Neutron activation analysis of hair from breast cancer patients

    International Nuclear Information System (INIS)

    Hair samples from breast cancer patients were collected at the same time as tumour and normal tissues obtained during mastectomy, in order to determine elemental concentrations and investigate whether hair can act as an epidemiological monitor of the disease. Instrumental neutron activation analysis was used and concentrations for Na, Mg, S, Cl, Ca, Mn, Cu, Zn, Br, I, Sb, Ba, Au and Hg in the hair samples measured. No strong correlations were found between the concentrations of Cl, Cu, Zn and Br in hair and those in tumour tissues and in normal tissues. The level of Zn in the patients hair is low and that of Ca very high

  20. 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.

  1. Assessment of computational methods for predicting the effects of missense mutations in human cancers

    OpenAIRE

    Gnad, Florian; Baucom, Albion; Mukhyala, Kiran; Manning, Gerard; Zhang, Zemin

    2013-01-01

    Background Recent advances in sequencing technologies have greatly increased the identification of mutations in cancer genomes. However, it remains a significant challenge to identify cancer-driving mutations, since most observed missense changes are neutral passenger mutations. Various computational methods have been developed to predict the effects of amino acid substitutions on protein function and classify mutations as deleterious or benign. These include approaches that rely on evolution...

  2. 3D analysis methods - Study and seminar

    International Nuclear Information System (INIS)

    The first part of the report results from a study that was performed as a Nordic co-operation activity with active participation from Studsvik Scandpower and Westinghouse Atom in Sweden, and VTT in Finland. The purpose of the study was to identify and investigate the effects rising from using the 3D transient com-puter codes in BWR safety analysis, and their influence on the transient analysis methodology. One of the main questions involves the critical power ratio (CPR) calculation methodology. The present way, where the CPR calculation is per-formed with a separate hot channel calculation, can be artificially conservative. In the investigated cases, no dramatic minimum CPR effect coming from the 3D calculation is apparent. Some cases show some decrease in the transient change of minimum CPR with the 3D calculation, which confirms the general thinking that the 1D calculation is conservative. On the other hand, the observed effect on neutron flux behaviour is quite large. In a slower transient the 3D effect might be stronger. The second part of the report is a summary of a related seminar that was held on the 3D analysis methods. The seminar was sponsored by the Reactor Safety part (NKS-R) of the Nordic Nuclear Safety Research Programme (NKS). (au)

  3. 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

    2006-01-01

    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.

  4. The incidence rate of corpus uteri cancer among females in Saudi Arabia: an observational descriptive epidemiological analysis of data from Saudi Cancer Registry 2001–2008

    Directory of Open Access Journals (Sweden)

    Alghamdi IG

    2014-01-01

    Full Text Available Ibrahim G Alghamdi,1 Issam I Hussain,1 Mohamed S Alghamdi,2 Mohamed A El-Sheemy1,3 1University of Lincoln, Brayford Pool, Lincoln, UK; 2Ministry of Health, General Directorate of Health Affairs, Al-Baha, Kingdom of Saudi Arabia; 3Research and Development, Lincoln Hospital, Lincolnshire Hospitals NHS Trust, Lincoln, UK Background: The present study reviews the epidemiological data on corpus uteri cancer among Saudi women, including its frequency, crude incidence rate, and age-standardized incidence rate (ASIR, adjusted by region and year of diagnosis. Methods: A retrospective, descriptive epidemiological analysis was conducted of all the corpus uteri cancer cases recorded in the Saudi Cancer Registry between January 2001 and December 2008. The statistical analyses were performed using descriptive statistics, analysis of variance, Poisson regression, and a simple linear model. Results: A total of 1,060 corpus uteri cancer cases were included. Women aged 60–74 years of age were most affected by the disease. The region of Riyadh in Saudi Arabia had the highest overall ASIR, at 4.4 cases per 100,000 female patients, followed by the eastern region, at 4.2, and Makkah, at 3.7. Jazan, Najran, and Qassim had the lowest average ASIRs, ranging from 0.8 to 1.4. A Poisson regression model using Jazan as the reference revealed that the corpus uteri cancer incidence rate ratio was significantly higher for the regions of Makkah, at 16.5 times (95% confidence interval [CI]: 8.0–23.0, followed by Riyadh, at 16.0 times (95% CI: 9.0–22.0, and the eastern region, at 9.9 times (95% CI: 5.6–17.6. The northern region experienced the highest changes in ASIRs of corpus uteri cancer among female Saudi patients between 2001 and 2008. Conclusion: There was a slight increase in the crude incidence rates and ASIRs for corpus uteri cancer in Saudi Arabia between 2001 and 2008. Older Saudi women were most affected by the disease. Riyadh, the eastern region, and Makkah

  5. Chapter 11. Community analysis-based methods

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Y.; Wu, C.H.; Andersen, G.L.; Holden, P.A.

    2010-05-01

    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.

  6. Methods to improve rehabilitation of patients following breast cancer surgery: a review of systematic reviews

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    Loh SY

    2015-03-01

    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

  7. Generalized Analysis of a Distribution Separation Method

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    Peng Zhang

    2016-04-01

    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.

  8. Preoperative transarterial chemoembolization for cervical cancer: analysis of efficacy

    International Nuclear Information System (INIS)

    Objective: To evaluate preoperative transarterial chemoembolization in treating locally advanced cervical cancer and to observe the pathological changes. Methods: Forty-three patients with pathologically proved cervical cancer were enrolled in this study. All patients were treated with transarterial chemoembolization before radical hysterectomy. Bleomycin and cisplantin were infused via bilateral uterine arteries, followed by arterial embolization with gelfoam particles as embolic agent. Radical hysterectomy was performed 20-87 days (mean 38.3 days) after chemoembolization, and the specimen was taken for pathologic examination. Results: (1) complete response (CR) was seen in 4 cases and partial response (PR) in 29 cases, with a total effective rate of 76.7%. (2) The interval between chemoembolization and hysterectomy was a risk factor related to the effect of chemoembolization, i.e. the longer the interval was, the poorer the effect of chemoembolization would be. (3) Pathologically, the tumoral parauterine infiltration was not so severe as estimated before surgery. Conclusion: Preoperative chemoembolization is a safe and effective adjunctive means for the treatment of cervical cancer, which is very helpful for the subsequent radical hysterectomy. (authors)

  9. [Contribution of lifestyle factors to cancer: secondary analysis of Dutch data over 2010 and a projection for 2020

    NARCIS (Netherlands)

    Lanting, C.I.; Vroome, E.M. de; Elias, S.G.; Brandt, P.A. van den; Leeuwen, F.E. van; Kampman, E.; Kiemeney, L.A.L.M.; Peeters, P.H.M.; Vries, E. de; Bausch-Goldbohm, R.A.

    2014-01-01

    OBJECTIVE: To calculate the proportion of cancer cases in the Netherlands in 2010 that were attributable to lifestyle factors by using the most recent data. DESIGN: Secondary analysis. METHOD: Lifestyle risk factors studied were tobacco smoking, alcohol consumption, overweight, lack of physical exer

  10. Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing

    DEFF Research Database (Denmark)

    Nygaard, Sanne; Jacobsen, Anders; Lindow, Morten;

    2009-01-01

    . METHODS: Here we describe the analysis of 454 pyrosequencing of small RNA from four different tissues: Breast cancer, normal adjacent breast, and two teratoma cell lines. We developed a pipeline for identifying new miRNAs, emphasizing extracting and retaining as much data as possible from even noisy...

  11. Bioinformatics Analysis for Coding SNPs of the HLADQA1 Gene Involved in Susceptibility to Cervical Cancer

    Institute of Scientific and Technical Information of China (English)

    Yanyun Li; Jun Xing; Linsheng Zhao; Yanni Li; Yuchuan Wang; Weiming Zhang

    2006-01-01

    OBJECTIVE To analyze coding SNPs of the HLA-DQA1 gene involved in susceptibility for cervical cancer by a bioinformatics approach, and to choose some SNPs that may have an association with cervical cancer.METHODS By a SNPper tool we extracted SNPs from a public database (dbSNP), exporting them in FASTA formats suitable for subsequent use.Then we used PARSESNP as a tool for the analysis of the cSNPs.RESULTS In the cSNPs of the HLA-DQA1 gene, we find that rs9272693and rs9272703, are made up of missense mutations which convert a codon for one amino acid into a codon for a different amino acid. We chose a PSSM Difference >10 as a lower level for the scores of changes predicted to be deldterious.CONCLUSION We used a bioinformatics approach for cSNPs analysis of the HLA-DQA1 gene. This method can select the variants in a conserved region, and give a PSSM Difference score. But the results need to be verified in cervical cancer patients and a control population.

  12. meta-analysis of the Relationship between Passive Smoking Population in China and Lung Cancer

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    Hui ZHAO

    2010-06-01

    Full Text Available Background and objective Studies of passive smoking exposure in China however are of particular interest, because of the high lung cancer rate in people who are mostly non-smokers. The aim of this study is to explore the relationship between passive smoking and lung cancer among non-smoking Chinese. Methods By searching Medline, PubMed, CENTRAL (the Cochrane central register of controlled trials, CBM, CNKI and VIP, et al, we collected both domestic and overseas published documents between 1987 and 2007 on passive smoking and lung cancer among non-smoking Chinese. Random or fixed effect models were applied to conduct meta-analysis on the case control study results, and the combined odds ratio (OR and the 95% confidence interval (CI were calculated as well. Results Sixteen documents were included into the combined analysis, which indicated that there was statistical significance between passive smoking and lung cancer (OR=1.13, 95%CI: 1.05-1.21, P=0.001. It was significant of lung cancer among non-smoking subjects associated with amount of tobacco passively smoked more than 20 cigarettes daily, with life period in adulthood passive smoking exposure, with gender female, and with exposure to workplace. The P value, OR and 95%CI were P=0.000 3, OR=1.78, 95%CI: 1.30-2.43; P=0.000 1, OR=1.50, 95%CI: 1.23-1.83; P=0.000 7, OR=1.50, 95%CI: 1.19-1.90; P<0.000 1, OR=1.41, 95%CI: 1.19-1.66; respectively. And there was no significant difference between passive smoking and lung cancer with amount of tobacco passively smoked within 20 cigarettes daily, with life period in childhood passive smoking exposure, with gender male and with exposure to spouse and parents. Conclusion Passive smoking is an important risk factor of lung cancer among non-smoking Chinese, and for non-smoking women who expose to environment tobacco smoke in a long period of time have a close relationship with lung cancer risk.

  13. Green tea consumption and risk of esophageal cancer: a meta-analysis of epidemiologic studies

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    Zheng Ping

    2012-11-01

    Full Text Available Abstract Background Green tea has shown the role of chemoprevention for cancer. Recently, several studies suggested that green tea intake may have effect on esophageal cancer risk, whereas the results were inconsistent. Methods We performed a meta-analysis of all English and Chinese language studies of green tea consumption and esophageal cancer risk indexed in Medline, Embase, the Science Citation Index, the Chinese Biomedical Database and Wanfang Data from 1980 to June 2012. After reviewing each study, extracting data, and evaluating heterogeneity (Chi-square-based Q test and Ι2 and publication bias (Begg and Egger test, a meta-analysis was performed to evaluate the association between high/medium/low green tea consumption and non-drinking esophageal cancer risk. Pooled relative risk (RR or odds ratio (OR with 95% confidence intervals (CIs were calculated using the fixed- or random-effect models. Results Ten eligible epidemiologic studies including 33731 participants and 3557 cases for esophageal cancer were included. Eight of which were case–control studies, and two were cohort studies. Overall, there were no association between high/medium/low green tea consumption and non-drinking risk of esophageal cancer (High: highest vs non-drinker: RR/OR = 0.76, 95% CI: 0.49 to 1.02. Medium: drinker vs non-drinker: RR/OR = 0.86, 95% CI: 0.70 to 1.03. Low: lowest vs non-drinker: RR/OR = 0.83, 95% CI: 0.58 to 1.08. When stratified analyses according to study design (case–control and cohort studies, country (China and Japan, participates source (population-based and hospital-based case–control, and gender (female and male, there were significant association between high/medium/low green tea consumption and non-drinking risk of esophageal cancer among female (High: RR/OR = 0.32, 95% CI: 0.10 to 0.54. Medium: RR/OR = 0.43, 95% CI: 0.21 to 0.66. Low: RR/OR = 0.45, 95% CI: 0.10 to 0.79, but not the others. Conclusions We did not found significant

  14. Comparative study of CEA and CA19-9 in esophageal, gastric and colon cancers individually and in combination (ROC curve analysis)

    Institute of Scientific and Technical Information of China (English)

    Bhawna Bagaria; Sadhna Sood; Rameshwaram Sharma; Soniya Lalwani

    2013-01-01

    Objective:To determine the clinical serum levels of carcinoembryonic antigen (CEA) and carbohydrate antigen 19-9 (CA19-9), individually and in combination, for the diagnosis of 50 healthy subjects and 150 cases of esophageal, gastric, and colon cancers. Methods:The sensitivities of the two markers were compared individually and in combination, with specificity set at 100%. Receiver operating characteristic (ROC) curves were plotted. Results:Serum CEA levels were significantly higher in cancer patients than in the control group. The sensitivity of CEA was determined:in esophageal cancer, sensitivity=28%, negative predictive value (NPV)=61.72%, and AUC=0.742 (SE=0.05), with a significance level of P Conclusion:CEA exhibited the highest sensitivity for colon cancer, and CA19-9 exhibited the highest sensitivity for gastric cancer. Combined analysis indicated an increase in diagnostic sensitivity in esophageal and gastric cancer compared with that in colon cancer.

  15. Marital status and survival in pancreatic cancer patients: a SEER based analysis.

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    Michael Baine

    Full Text Available BACKGROUND: Recent findings suggest that marital status affects survival in patients with different types of cancer. However, its role in the survival of patients with pancreatic ductal adenocarcinoma is unknown. In this study, we investigated whether there was an association between marital status and overall survival (OS in patients with pancreatic ductal adenocarcinoma (PDAC. METHODS: Adult patients diagnosed with PDAC between 1998 and 2003 with known marital statuses were identified from the Surveillance, Epidemiology, and End Results registry of the National Cancer Institute. OS for these patients was plotted using the Kaplan-Meier method. Comparative risks of mortality were evaluated by using univariate and multivariate-adjusted Cox regression models. RESULTS: Using Kaplan-Meier analysis, we found that the median overall survival of patients was 4 months and 3 months (p<0.001 for married and unmarried patients, respectively. Subgroup analysis on patients with cancer-directed surgery showed that the median survival was 16 months and 13 months (P<0.0005 for married and unmarried groups, respectively. Multivariate analysis adjusting for age, race, sex, stage, year of diagnosis, radiation therapy and cancer-directed surgery showed that patients who were married at the time of diagnosis had a significantly decreased risk of death at both 2 months (15% risk reduction and 3 years (13% risk reduction post diagnosis. CONCLUSIONS: Marital status is an independent prognostic factor of both perioperative and long-term survival in patients with PDAC. This observation may suggest a suboptimally met psychosocial need among PDAC patients that is partially fulfilled by the support system provided by marriage.

  16. Novel Method for Detection of Gastric Cancer by Hyperspectral Image Technique

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    Preetha Nair

    2014-01-01

    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 co