The need for new methods to backcalculate soil cleanup targets in interval and probabilistic cancer risk assessments

Ordinary algebra may be used to backcalculate health‐based cleanup targets in deterministic risk assessments, but it does not work in interval or probabilistic risk assessments. Equations with interval or random variables do not follow the rules of ordinary algebra. This paper explains the need for more sophisticated methods to backcalculate soil cleanup targets when using interval or random variables.     

The infinitesimal, the deterministic, and the probabilistic: Alternate container inspection policies in invasive species management

Recently, Batabyal and Nijkamp (2005, Stochastic Environmental Research and Risk Assessment 19: 340–347) have shown that in an inspection cycle, regardless of whether the inspection policy choice is made on the basis of an optimization exercise or on the basis of a rule of thumb, the “container policy” dominates the “temporal policy” because the former results in lower long run expected net cost (LRENC) from inspections. In this paper, we continue this line of inquiry and analyze container policies in three scenarios. In the first scenario the time taken to conduct inspections is negligible. In the second scenario, this inspection time is deterministic and in the third scenario this inspection time is stochastic. Specifically, we compare and contrast the LRENC and the optimal container policy in each of these three scenarios.      

Mathematical properties of the risk equation when variability is present

When random variables are used to represent variability, the risk equation has mathematical properties poorly understood by many risk assessors, variability represents the heterogeneity in a well‐characterized population, usually not reducible through further measurement or study. We follow the lead of most mathematicians in using random variables to represent and analyze variability. To illustrate the issues, we use LogNormal distributions to model variability.     

The risk of flawed inference in evolutionary studies when detectability is less than one

Addressing evolutionary questions in the wild remains a challenge. It is best done by monitoring organisms from birth to death, which is very difficult in part because individuals may or may not be resighted or recaptured. Although the issue of uncertain detection has long been acknowledged in ecology and conservation biology, in evolutionary studies of wild populations it is often assumed that detectability is perfect. We argue that this assumption may lead to flawed inference. We demonstrate that the form of natural selection acting on body mass of sociable weavers is altered and that the rate of senescence of roe deer is underestimated when not accounting for a value of detectability that is less than one. Because mark-recapture models provide an explicit way to integrate and reliably model the detection process, we strongly recommend their use to address questions in evolutionary biology.     

A method for determining weights for excess relative risk and excess absolute risk when applied in the calculation of lifetime risk of cancer from radiation exposure

Radiation-related risks of cancer can be transported from one population to another population at risk, for the purpose of calculating lifetime risks from radiation exposure. Transfer via excess relative risks (ERR) or excess absolute risks (EAR) or a mixture of both (i.e., from the life span study (LSS) of Japanese atomic bomb survivors) has been done in the past based on qualitative weighting. Consequently, the values of the weights applied and the method of application of the weights (i.e., as additive or geometric weighted means) have varied both between reports produced at different times by the same regulatory body and also between reports produced at similar times by different regulatory bodies. Since the gender and age patterns are often markedly different between EAR and ERR models, it is useful to have an evidence-based method for determining the relative goodness of fit of such models to the data. This paper identifies a method, using Akaike model weights, which could aid expert judgment and be applied to help to achieve consistency of approach and quantitative evidence-based results in future health risk assessments. The results of applying this method to recent LSS cancer incidence models are that the relative EAR weighting by cancer solid cancer site, on a scale of 0–1, is zero for breast and colon, 0.02 for all solid, 0.03 for lung, 0.08 for liver, 0.15 for thyroid, 0.18 for bladder and 0.93 for stomach. The EAR weighting for female breast cancer increases from 0 to 0.3, if a generally observed change in the trend between female age-specific breast cancer incidence rates and attained age, associated with menopause, is accounted for in the EAR model. Application of this method to preferred models from a study of multi-model inference from many models fitted to the LSS leukemia mortality data, results in an EAR weighting of 0. From these results it can be seen that lifetime risk transfer is most highly weighted by EAR only for stomach cancer. However, the generalization and interpretation of radiation effect estimates based on the LSS cancer data, when projected to other populations, are particularly uncertain if considerable differences exist between site-specific baseline rates in the LSS and the other populations of interest. Definitive conclusions, regarding the appropriate method for transporting cancer risks, are limited by a lack of knowledge in several areas including unknown factors and uncertainties in biological mechanisms and genetic and environmental risk factors for carcinogenesis; uncertainties in radiation dosimetry; and insufficient statistical power and/or incomplete follow-up in data from radio-epidemiological studies.     

不同经营管理方式下锥栗林节肢动物群落的时序动态

【目的】研究不同经营管理方式对锥栗林(Castanea henryi)节肢动物群落及主要害虫种群数量时序动态的影响,为锥栗林害虫防治提供科学依据。【方法】通过对不同经营管理方式下的锥栗林节肢动物群落的系统调查,分析和比较了生产上典型的5种经营管理方式下锥栗林节肢动物群落的物种丰富度、个体数量、物种多样性指数、天敌与害虫个体数量比例及主要害虫种群数量的时序动态。【结果】不同经营管理方式下锥栗林林冠层节肢动物群落的物种丰富度、个体数量、物种多样性指数变化趋势大体一致,物种丰富度、个体数量最高值在6月,物种多样性指数最高值在5月,但不同经营管理方式下物种丰富度、个体数量、物种多样性指数高低不同,管理精细未用药型锥栗林物种多样性指数最高,管理撂荒型的物种丰富度、个体数量最高;相对锥栗林管理撂荒型,其它各种经营管理方式都明显地降低了下木层的物种丰富度、个体数量、物种多样性指数,不同经营管理方式下下木层物种丰富度、个体数量、物种多样性指数的动态变化相差较大;管理精细未用药型林冠层天敌与害虫个体数量比例相对最高,波动变化较大,自然控害能力最强;管理精细的锥栗林主要害虫栗瘿蜂Dryocosmus kuriphilus(Yasumatus)、栗实象Curculio davidi Fairmaire、栗链蚧Asterolecanium castaneae(Russell)种群数量显著低于管理撂荒和管理粗放的锥栗林。【结论】不同经营管理方式对锥栗林节肢动物群落及主要害虫种群数量的时序动态有较大影响,对锥栗林科学的精细管理有助于对主要害虫的有效控制。     

The loss in power when the test of differential expression is performed under a wrong scale.

One of the most common and important goals of microarray studies is to identify genes that are differentially expressed between cells of different conditions. T-test and ANOVA models on the expression data are common practices to gauge the significance of the observed difference in expression levels. Transformation of the microarray data is often applied in order to satisfy the model assumptions being entertained. However, the distributional properties of the expression are gene specific, and it is impractical to find a single transformation that is universally optimal for all the genes. This difficulty results in the situation that some genes have to violate the assumptions of the model (e.g., homogeneity in variance, normality). It is thus the interest of this paper to evaluate the impact on the inference of differential expression when the test is performed under an inappropriate scale. Particularly, we quantitatively assess the loss of power when the test is performed under a wrong scale. Normal distribution and log-normal distribution of the expression data are considered. The loss in power is investigated in two scenarios: a transformation is misused, or a transformation fails to be applied. Log transformation and power transformation are particularly considered due to the fact that Box-Cox types of transformation are commonly used in practice. The impact of using a wrong scale is investigated analytically and based on simulations. The loss in power is assessed both as a function of the degree to which the assumptions are violated and as a function of the effect size. Simulations are conducted to quantitatively assess the power loss when tests are performed under a wrong scale. A public experimental microarray dataset is used to illustrate the impact of transformation on the results of testing differential expression. The results show that the loss of power is a function of CV and fold-change (effect size). The loss in power depends on the true model and on how severely the assumptions are violated.     

Psychological outcomes of different treatment policies in women with early breast cancer outside a clinical trial.

OBJECTIVES--To assess outside a clinical trial the psychological outcome of different treatment policies in women with early breast cancer who underwent either mastectomy or breast conservation surgery depending on the surgeon''s opinion or the patient''s choice. To determine whether the extent of psychiatric morbidity reported in women who underwent breast conservation surgery was associated with their participation in a randomised clinical trial. DESIGN--Prospective, multicentre study capitalising on individual and motivational differences among patients and the different management policies among surgeons for treating patients with early breast cancer. SETTING--12 District general hospitals, three London teaching hospitals, and four private hospitals. PATIENTS--269 Women under 75 with a probable diagnosis of stage I or II breast cancer who were referred to 22 different surgeons. INTERVENTIONS--Surgery and radiotherapy or adjuvant chemotherapy, or both, depending on the individual surgeon''s stated preferences for managing early breast cancer. MAIN OUTCOME MEASURES--Anxiety and depression as assessed by standard methods two weeks, three months, and 12 months after surgery. RESULTS--Of the 269 women, 31 were treated by surgeons who favoured mastectomy, 120 by surgeons who favoured breast conservation, and 118 by surgeons who offered a choice of treatment. Sixty two of the women treated by surgeons who offered a choice were eligible to choose their surgery, and 43 of these chose breast conserving surgery. The incidences of anxiety, depression, and sexual dysfunction were high in all treatment groups. There were no significant differences in the incidences of anxiety and depression between women who underwent mastectomy and those who underwent lumpectomy. A significant effect of surgeon type on the incidence of depression was observed, with patients treated by surgeons who offered a choice showing less depression than those treated by other surgeons (p = 0.06). There was no significant difference in psychiatric morbidity between women treated by surgeons who offered a choice who were eligible to choose their treatment and those in the same group who were not able to choose. Most of the women (159/244) gave fear of cancer as their primary fear rather than fear of losing a breast. The overall incidences of psychiatric morbidity in women who underwent mastectomy and those who underwent lumpectomy were similar to those found in the Cancer Research Campaign breast conservation study. At 12 months 28% of women who underwent mastectomy in the present study were anxious compared with 26% in the earlier study, and 27% of women in the present study who underwent lumpectomy were anxious compared with 31% in the earlier study. In both the present and earlier study 21% of women who underwent mastectomy were depressed, and 19% of women who underwent lumpectomy in the present study were depressed compared with 27% in the earlier study.) CONCLUSIONS--There is still no evidence that women with early breast cancer who undergo breast conservation surgery have less psychiatric morbidity after treatment than those who undergo mastectomy. Women who surrender autonomy for decision making by agreeing to participate in randomised clinical trials do not experience any different psychological, sexual, or social problems from those women who are treated for breast cancer outside a clinical trial.     

Growth of cancer cell lines under stem cell-like conditions has the potential to unveil therapeutic targets

Malignant tumors comprise a small proportion of cancer-initiating cells (CIC), capable of sustaining tumor formation and growth. CIC are the main potential target for anticancer therapy. However, the identification of molecular therapeutic targets in CIC isolated from primary tumors is an extremely difficult task. Here, we show that after years of passaging under differentiating conditions, glioblastoma, mammary carcinoma, and melanoma cell lines contained a fraction of cells capable of forming spheroids upon in vitro growth under stem cell-like conditions. We found an increased expression of surface markers associated with the stem cell phenotype and of oncogenes in cell lines and clones cultured as spheroids vs. adherent cultures. Also, spheroid-forming cells displayed increased tumorigenicity and an altered pattern of chemosensitivity. Interestingly, also from single retrovirally marked clones, it was possible to isolate cells able to grow as spheroids and associated with increased tumorigenicity. Our findings indicate that short-term selection and propagation of CIC as spheroid cultures from established cancer cell lines, coupled with gene expression profiling, represents a suitable tool to study and therapeutically target CIC: the notion of which genes have been down-regulated during growth under differentiating conditions will help find CIC-associated therapeutic targets.     

A stress protein is induced in the deep-sea barophilic hyperthermophile Thermococcus barophilus when grown under atmospheric pressure

The whole-cell protein inventory of the deep-sea barophilic hyperthermophile Thermococcus barophilus was examined by one-dimensional SDS gradient gel electrophoresis when grown under different pressure conditions at 85°C (T _opt). One protein (P60) with a molecular mass of approximately 60 kDa was prominent at low pressures (0.3 MPa hydrostatic pressure and 0.1 MPa atmospheric pressure) but not at deep-sea pressures (10, 30, and 40 MPa). About 17 amino acids were sequenced from the N-terminal end of the protein. Sequence homology analysis in the GenBank database showed that P60 most closely resembled heat-shock proteins in some sulfur-metabolizing Archaea. A high degree of amino acid identity (81%–93%) to thermosome subunits in Thermococcales strains was found. Another protein (P35) with molecular mass of approximately 35.5 kDa was induced at 40 MPa hydrostatic pressure but not under low-pressure conditions. No amino acid sequence homology was found for this protein when the 40 amino acids from the N-terminal end were compared with homologous regions of proteins from databases. A PTk diagram was generated for T. barophilus. The results suggest that P _habitat is about 35 MPa, which corresponds to the in situ pressure where the strain was obtained. Received: May 14, 1999 / Accepted: July 30, 1999     

The potential to mitigate global warming with no-tillage management is only realized when practised in the long term

No‐tillage (NT) management has been promoted as a practice capable of offsetting greenhouse gas (GHG) emissions because of its ability to sequester carbon in soils. However, true mitigation is only possible if the overall impact of NT adoption reduces the net global warming potential (GWP) determined by fluxes of the three major biogenic GHGs (i.e. CO₂, N₂O, and CH₄). We compiled all available data of soil‐derived GHG emission comparisons between conventional tilled (CT) and NT systems for humid and dry temperate climates. Newly converted NT systems increase GWP relative to CT practices, in both humid and dry climate regimes, and longer‐term adoption (>10 years) only significantly reduces GWP in humid climates. Mean cumulative GWP over a 20‐year period is also reduced under continuous NT in dry areas, but with a high degree of uncertainty. Emissions of N₂O drive much of the trend in net GWP, suggesting improved nitrogen management is essential to realize the full benefit from carbon storage in the soil for purposes of global warming mitigation. Our results indicate a strong time dependency in the GHG mitigation potential of NT agriculture, demonstrating that GHG mitigation by adoption of NT is much more variable and complex than previously considered, and policy plans to reduce global warming through this land management practice need further scrutiny to ensure success.     

Comparison of methods to investigate microbial populations in soils under different agricultural management

As water is a source of nosocomial infections in hospitals, the presence of fastidious Gram-negative bacteria in water samples taken in a university hospital was investigated. Water samples were inoculated onto agar plates and into amoebal microplates for co-culture. Sixty-eight alpha proteobacteria isolates were obtained and characterized using phenotypic methods and 16S rRNA gene sequence comparison. The latter approach divided the strains into seven clusters. Of these, one corresponded to previously recognized Afipia felis and it is likely that six were closely related new species. As these bacteria are fastidious and can not be cultivated on standard microbiological media, their possible role in hospital-acquired human infections should be investigated.     

Anaplastic lymphoma kinase is expressed in different subtypes of human breast cancer

Pleiotrophin (PTN, Ptn) is an 18kDa cytokine expressed in human breast cancers. Since inappropriate expression of Ptn stimulates progression of breast cancer in transgenic mice and a dominant negative PTN reverses the transformed phenotype of human breast cancer cells that inappropriately express Ptn, it is suggested that constitutive PTN signaling in breast cancer cells that inappropriately express Ptn activates pathways that promote a more aggressive breast cancer phenotype. Pleiotrophin signals by inactivating its receptor, the receptor protein tyrosine phosphatase (RPTP)beta/zeta, and, recently, PTN was found to activate anaplastic lymphoma kinase (ALK) through the PTN/RPTPbeta/zeta signaling pathway in PTN-stimulated cells, not through a direct interaction of PTN with ALK and thus not through the PTN-enforced dimerization of ALK. Since full-length ALK is activated in different malignant cancers and activated ALK is a potent oncogenic protein, we examined human breast cancers to test the possibility that ALK may be expressed in breast cancers and potentially activated through the PTN/RPTPbeta/zeta signaling pathway; we now demonstrate that ALK is strongly expressed in different histological subtypes of human breast cancer; furthermore, ALK is expressed in both nuclei and cytoplasm and, in the ;;dotted" pattern characteristic of ALK fusion proteins in anaplastic large cell lymphoma. This study thus supports the possibility that activated ALK may be important in human breast cancers and potentially activated either through the PTN/RPTPbeta/zeta signaling pathway, or, alternatively, as an activated fusion protein to stimulate progression of breast cancer in humans.     

Comparison of maximum statistics for hypothesis testing when a nuisance parameter is present only under the alternative

In many practical problems, a hypothesis testing involves a nuisance parameter which appears only under the alternative hypothesis. Davies (1977, Biometrika 64, 247-254) proposed the maximum of the score statistics over the whole range of the nuisance parameter as a test statistic for this type of hypothesis testing. Freidlin, Podgor, and Gastwirth (1999, Biometrics 55, 883-886) studied two other simpler maximum test statistics, the maximum of the score statistics at two extreme points of the nuisance parameter, and the maximum of the score statistics at three points of the nuisance parameter including the two extreme points. In this article, we compare the powers of these three maximum-type statistics in the context of three genetic problems.     

On the possibility of improving the efficiency of cancer recognition and eradication in vivo when concurrently using two different types of nanodevices

When using nanodevices in oncology, it is necessary to provide efficiency of the performance of these nanodevices simultaneously with their safety for an organism. These are conflicting objectives to some extent. Nevertheless, as shown in this work, an approach that helps to eliminate this contradiction is offered. For recognition and destruction of cancer cells in vivo it is suggested to use, instead of one type, simultaneously two types of specialized nanodevices interacting with each other introduced into an organism. Some of the nanodevices only recognize cancer cells, while other ones, that cannot recognize them, find cells being marked by nanodevices of the first type, and destroy them. This makes it possible to increase the reliability of the cancer cell recognition process on the one hand, and have the process of their destruction rather safe for an organism on the other hand.     

Mutagens in the feces of 3 South-African populations at different levels of risk for colon cancer.

The incidence of mutagens in the feces of 3 South-African populations at different risk levels for colon cancer has been determined. Lyophilized fecal samples were extracted with ether and the mutagenicity of the extracts determined using the Salmonella/mammalian microsome mutagenicity test. 19% of the samples from urban white South-Africans, a population at a high risk for colon cancer, were mutagenic using Salmonella typhimurium strain TA100. This incidence was significantly greater (p less than 0.001) than the incidence of mutagen excretion in the low-risk populations of urban blacks (2%) and rural blacks (0%). This pattern was also obtained using Salmonella typhimurium strain TA98. The incidence of mutagen excretion for urban whites was 10%, as compared to 5% and 2% for urban and rural blacks, respectively.