CSNL: A cost-sensitive non-linear decision tree algorithm

This article presents a new decision tree learning algorithm called CSNL that induces Cost-Sensitive Non-Linear decision trees. The algorithm is based on the hypothesis that nonlinear decision nodes provide a better basis than axis-parallel decision nodes and utilizes discriminant analysis to construct nonlinear decision trees that take account of costs of misclassification. The performance of the algorithm is evaluated by applying it to seventeen datasets and the results are compared with those obtained by two well known cost-sensitive algorithms, ICET and MetaCost, which generate multiple trees to obtain some of the best results to date. The results show that CSNL performs at least as well, if not better than these algorithms, in more than twelve of the datasets and is considerably faster. The use of bagging with CSNL further enhances its performance showing the significant benefits of using nonlinear decision nodes. The performance of the algorithm is evaluated by applying it to seventeen data sets and the results are compared with those obtained by two well known cost-sensitive algorithms, ICET and MetaCost, which generate multiple trees to obtain some of the best results to date. The results show that CSNL performs at least as well, if not better than these algorithms, in more than twelve of the data sets and is considerably faster. The use of bagging with CSNL further enhances its performance showing the significant benefits of using non-linear decision nodes

Anthropometric factors and breast cancer risk among urban and rural women in South India: a multicentric case–control study

Breast cancer (BC) incidence in India is approximately twice as high in urban women than in rural women, among whom we investigated the role of anthropometric factors and body size. The study was conducted at the Regional Cancer Centre, Trivandrum, and in three cancer hospitals in Chennai during 2002–2005. Histologically confirmed cases (n=1866) and age-matched controls (n=1873) were selected. Anthropometric factors were measured in standard ways. Information on body size at different periods of life was obtained using pictograms. Odds ratios (OR) of BC were estimated through logistic regression modelling. Proportion of women with body mass index (BMI)>25.0 kg/m2, waist size >85 cm and hip size >100 cm was significantly higher among urban than rural women. Risk was increased for waist size >85 cm (pre-menopausal: OR=1.24, 95% CI: 0.96–1.62; post-menopausal: 1.61, 95% CI: 1.22–2.12) and hip size >100 cm (pre-menopausal: OR=1.47, 95% CI: 1.05–2.06; post-menopausal 2.42, 95% CI: 1.72–3.41). Large body size at age 10 (OR=1.75, 95% CI: 1.01–3.03) and increased BMI (OR=1.33, 95% CI: 1.05–1.69 for 25.0–29.9 kg/m2 and OR=1.56, 95% CI: 1.03–2.35 for 30+ kg/m2) were associated with pre-menopausal BC risk. Our data support the hypotheses that increased anthropometric factors are risk factors of BC in India

A study of soft tissue sarcomas after childhood cancer in Britain

Among 16 541 3-year survivors of childhood cancer in Britain, 39 soft tissue sarcomas (STSs) occurred and 1.1 sarcomas were expected, yielding a standardised incidence ratio (SIR) of 16.1. When retinoblastomas were excluded from the cohort, the SIR for STSs was 15.9, and the cumulative risk of developing a soft tissue tumour after childhood cancer within 20 years of 3-year survival was 0.23%. In the case–control study, there was a significant excess of STSs in those patients exposed to both radiotherapy (RT) and chemotherapy, which was five times that observed among those not exposed (P=0.02). On the basis of individual radiation dosimetry, there was evidence of a strong dose–response effect with a significant increase in the risk of STS with increasing dose of RT (P<0.001). This effect remained significant in a multivariate model. The adjusted risk in patients exposed to RT doses of over 3000 cGy was over 50 times the risk in the unexposed. There was evidence of a dose–response effect with exposure to alkylating agents, the risk increasing substantially with increasing cumulative dose (P=0.05). This effect remained after adjusting for the effect of radiation exposure

Differential disgust responding in people with cancer and implications for psychological wellbeing

Objectives: Evidence suggests that disgust responses, known to negatively affect psychological wellbeing, may differ in people with cancer. We performed the first quantitative investigation of three discrete types of disgust trait - disgust propensity, sensitivity, and self-directed disgust - in people diagnosed with a broad range of cancers (versus cancer-free controls), and explored their associations with psychological wellbeing. Design: In a cross-sectional survey design, 107 participants with heterogeneous cancer diagnoses, recruited from cancer charities and support groups, were matched with cancer-free controls by age and gender. Outcome measures: Measures of the three disgust traits were taken alongside measures of anxiety and depression. Results: Disgust sensitivity and physical self-disgust were significantly higher in the cancer than control sample, while disgust propensity and behavioural self-disgust were lower. The disgust traits had a different pattern of associations to psychological wellbeing across the two groups, with disgust sensitivity predicting depressive symptoms to a significantly greater extent in the cancer than control group. Conclusions: People with cancer differ from matched controls in their disgust responses and these responses have significant predictive relationships with aspects of their psychological wellbeing. The results suggest that emotion-based interventions may be useful for improving psychological wellbeing in people with cancer

Empirical evaluation of prediction intervals for cancer incidence

BACKGROUND: Prediction intervals can be calculated for predicting cancer incidence on the basis of a statistical model. These intervals include the uncertainty of the parameter estimates and variations in future rates but do not include the uncertainty of assumptions, such as continuation of current trends. In this study we evaluated whether prediction intervals are useful in practice. METHODS: Rates for the period 1993–97 were predicted from cancer incidence rates in the five Nordic countries for the period 1958–87. In a Poisson regression model, 95% prediction intervals were constructed for 200 combinations of 20 cancer types for males and females in the five countries. The coverage level was calculated as the proportion of the prediction intervals that covered the observed number of cases in 1993–97. RESULTS: Overall, 52% (104/200) of the prediction intervals covered the observed numbers. When the prediction intervals were divided into quartiles according to the number of cases in the last observed period, the coverage level was inversely proportional to the frequency (84%, 52%, 46% and 26%). The coverage level varied widely among the five countries, but the difference declined after adjustment for the number of cases in each country. CONCLUSION: The coverage level of prediction intervals strongly depended on the number of cases on which the predictions were based. As the sample size increased, uncertainty about the adequacy of the model dominated, and the coverage level fell far below 95%. Prediction intervals for cancer incidence must therefore be interpreted with caution

The cumulative risk of lung cancer among current, ex- and never-smokers in European men

Recent analyses based on UK data indicate that people who stop smoking, even well into middle age, avoid most of their subsequent risk of lung cancer. We investigated whether similar absolute risks of lung cancer in men are found in other European countries with different smoking patterns and at different stages of their lung cancer epidemic. Using data for men from a multicentre case-control study of lung cancer in the UK, Germany, Italy and Sweden, and including 6523 lung cancer cases and 9468 controls, we combined odds ratio estimates with estimates of national lung cancer incidence rates to calculate the cumulative risk of lung cancer among men by age 75. Lung cancer cumulative risks by age 75 among continuing smokers were similar for the UK, Germany and Italy at 15.7, 14.3 and 13.8% respectively, whereas the cumulative risk among Swedish male smokers was 6.6%. The proportion of the risk of lung cancer avoided by quitting smoking before the age of 40 was comparable between the four countries, at 80% in Italy and 91% in the UK, Germany and Sweden. Similarly, the proportion of the excess risk avoided by quitting before the age of 50 ranged from 57% in Italy to 69% in Germany. Our results support the important conclusion that for long-term smokers, giving up smoking in middle age avoids most of the subsequent risk of lung cancer, and that lung cancer mortality in European men over the next three decades will be determined by the extent to which current smokers can successfully quit smoking

First and subsequent asbestos exposures in relation to mesothelioma and lung cancer mortality

We analysed data from a cohort of 1966 subjects (889 men and 1077 women) employed by an Italian asbestos (mainly textile) company in the period 1946–1984, who were followed-up to 2004. A total of 62 025 person-years of observation were recorded. We computed standardised mortality ratios (SMR) for all causes and selected cancer sites using national death rates for each 5-year calendar period and age group. There were 68 deaths from mesothelioma (25 men and 43 women, 39 pleural and 29 peritoneal) vs 1.6 expected (SMR=4159), and 109 from lung cancer vs 35.1 expected (SMR=310). The SMRs of pleural/peritoneal cancer were 6661 for subjects exposed only before 30 years of age, 8019 for those first exposed before 30 and still employed at 30–39 years of age and 5786 for those first exposed before 30 and still employed at 40 or more years of age. The corresponding SMRs for lung cancer were 227, 446 and 562. The SMR of mesothelioma was strongly related to time since first exposure. The SMR of lung cancer, but not of mesothelioma, appeared to be related to subsequent exposures

Collection of population-based cancer staging information in Western Australia – a feasibility study

BACKGROUND: Routine data from cancer registries often lack information on stage of cancer, limiting their use. This study aimed to determine whether or not it is feasible to add cancer staging data to the routine data collections of a population-based Western Australian Cancer Registry (WACR). METHODS: For each of the five most common cancer types (prostate, colorectal, melanoma, breast and lung cancers), 60 cases were selected for staging. For the 15 next most common cancer types, 20 cases were selected. Four sources for collecting staging data were used in the following order: the WACR, the hospital based cancer registries (HBCRs), hospital medical records, and letters to treating doctors. If the case was unable to be fully staged, due to lack of information on regional lymph node invasion or distant metastases, we made the following assumptions. Cases which had data available for tumour (T) and regional lymph nodes (N), but no assessment of distant metastasis (MX) were assumed to have no distant metastases (M0). Cases which had data for T and M, but no assessment of regional nodal involvement (NX) were assumed to have no regional nodal involvement (N0). RESULTS: The main focus of this project was the process of collecting staging data, and not the outcomes. For ovary, cervix and uterus cancers the existence of a HBCR increased the stageable proportion of cases so that staging data for these cancers could be incorporated into the WACR immediately. Breast and colorectal cancer could also be staged with adequate completeness if it were assumed that MX = M0. Similarly, melanoma and prostate cancer could be staged adequately if it were assumed that NX = N0 and MX = M0. Some cases of stomach, lung, pancreas, thyroid, testis and kidney cancers could be staged, but additional clinical input – on pathology request forms, for example – would be required to achieve useable levels of completeness. For the remaining cancer types either staging is widely regarded as not relevant, and no generally-accepted system exists, or an acceptable level of completeness is not achievable. CONCLUSION: Adding stage to routinely collected information in a cancer registry is possible for many cancer types, particularly if the assumptions regarding missing data are found to be acceptable or if the guidelines for MX = M0 asumptions are clarified. These findings should be generalizable to most cancer registries in developed countries, if hospital-based cancer registries or other specialized databases are accessible

Highly Conducting pi-Conjugated Molecular Junctions Covalently Bonded to Gold Electrodes

We measure electronic conductance through single conjugated molecules bonded to Au metal electrodes with direct Au-C covalent bonds using the scanning tunneling microscope based break-junction technique. We start with molecules terminated with trimethyltin end groups that cleave off in situ resulting in formation of a direct covalent sigma bond between the carbon backbone and the gold metal electrodes. The molecular carbon backbone used in this study consist of a conjugated pi-system that has one terminal methylene group on each end, which bonds to the electrodes, achieving large electronic coupling of the electrodes to the pi-system. The junctions formed with the prototypical example of 1,4-dimethylenebenzene show a conductance approaching one conductance quantum (G0 = 2e2/h). Junctions formed with methylene terminated oligophenyls with two to four phenyl units show a hundred-fold increase in conductance compared with junctions formed with amine-linked oligophenyls. The conduction mechanism for these longer oligophenyls is tunneling as they exhibit an exponential dependence of conductance with oligomer length. In addition, density functional theory based calculations for the Au-xylylene-Au junction show near-resonant transmission with a cross-over to tunneling for the longer oligomers.Comment: Accepted to the Journal of the American Chemical Society as a Communication