High-resolution microarray analysis of chromosome 20q in human colon cancer metastasis model systems

Amplification of human chromosome 20q DNA is the most frequently occurring chromosomal abnormality detected in sporadic colorectal carcinomas and shows significant correlation with liver metastases. Through comprehensive high-resolution microarray comparative genomic hybridization and microarray gene expression profiling, we have characterized chromosome 20q amplicon genes associated with human colorectal cancer metastasis in two in vitro metastasis model systems. The results revealed increasing complexity of the 20q genomic profile from the primary tumor-derived cell lines to the lymph node and liver metastasis derived cell lines. Expression analysis of chromosome 20q revealed a subset of over expressed genes residing within the regions of genomic copy number gain in all the tumor cell lines, suggesting these are Chromosome 20q copy number responsive genes. Bases on their preferential expression levels in the model system cell lines and known biological function, four of the over expressed genes mapping to the common intervals of genomic copy gain were considered the most promising candidate colorectal metastasis-associated genes. Validation of genomic copy number and expression array data was carried out on these genes, with one gene, DNMT3B, standing out as expressed at a relatively higher levels in the metastasis-derived cell lines compared with their primary-derived counterparts in both the models systems analyzed. The data provide evidence for the role of chromosome 20q genes with low copy gain and elevated expression in the clonal evolution of metastatic cells and suggests that such genes may serve as early biomarkers of metastatic potential. The data also support the utility of the combined microarray comparative genomic hybridization and expression array analysis for identifying copy number responsive genes in areas of low DNA copy gain in cancer cells. ^

Clergy in support of gays, Left-right: Rev. C. Edward Egan Jr., Rev. Roy Birchard, Rev. Robert E. Carter S.J., Rev. Gerad Lee, O.F.M., Rev. John D. Carnwale, O.F.M.

General note: Title and date provided by Bettye Lane.

Bronchus-Associated Lymphoid Tissue (BALT) and Survival in a Vaccine Mouse Model of Tularemia

Background: Francisella tularensis causes severe pulmonary disease, and nasal vaccination could be the ideal measure to effectively prevent it. Nevertheless, the efficacy of this type of vaccine is influenced by the lack of an effective mucosal adjuvant. Methodology/Principal Findings: Mice were immunized via the nasal route with lipopolysaccharide isolated from F. tularensis and neisserial recombinant PorB as an adjuvant candidate. Then, mice were challenged via the same route with the F. tularensis attenuated live vaccine strain (LVS). Mouse survival and analysis of a number of immune parameters were conducted following intranasal challenge. Vaccination induced a systemic antibody response and 70% of mice were protected from challenge as showed by their improved survival and weight regain. Lungs from mice recovering from infection presented prominent lymphoid aggregates in peribronchial and perivascular areas, consistent with the location of bronchus-associated lymphoid tissue (BALT). BALT areas contained proliferating B and T cells, germinal centers, T cell infiltrates, dendritic cells (DCs). We also observed local production of antibody generating cells and homeostatic chemokines in BALT areas. Conclusions: These data indicate that PorB might be an optimal adjuvant candidate for improving the protective effect of F. tularensis antigens. The presence of BALT induced after intranasal challenge in vaccinated mice might play a role in regulation of local immunity and long-term protection, but more work is needed to elucidate mechanisms that lead to its formation.

Intermediate motions and dipolar couplings as studied by Lee-Goldburg cross-polarization NMR: Hartmann-Hahn matching profiles

In this article, we evaluate the use of simple Lee-Goldburg cross-polarization (LG-CP) NMR experiments for obtaining quantitative information of molecular motion in the intermediate regime. In particular, we introduce the measurement of Hartmann-Hahn matching profiles for the assessment of heteronuclear dipolar couplings as well as dynamics as a reliable and robust alternative to the more common analysis of build-up curves. We have carried out dynamic spin dynamics simulations in order to test the method's sensitivity to intermediate motion and address its limitations concerning possible experimental imperfections. We further demonstrate the successful use of simple theoretical concepts, most prominently Anderson-Weiss (AW) theory, to analyze the data. We further propose an alternative way to estimate activation energies of molecular motions, based upon the acquisition of only two LG-CP spectra per temperature at different temperatures. As experimental tests, molecular jumps in imidazole methyl sulfonate, trimethylsulfoxonium iodide, and bisphenol A polycarbonate were investigated with the new method.

A Model for comparing reduced impact logging with conventional logging for an Eastern Amazonian Forest

Using data from a logging experiment in the eastern Brazilian Amazon region, we develop a matrix growth and yield model that captures the dynamic effects of harvest system choice on forest structure and composition. Multinomial logistic regression is used to estimate the growth transition parameters for a 10-year time step, while a Poisson regression model is used to estimate recruitment parameters. The model is designed to be easily integrated with an economic model of decisionmaking to perform tropical forest policy analysis. The model is used to compare the long-run structure and composition of a stand arising from the choice of implementing either conventional logging techniques or more carefully planned and executed reduced-impact logging (RIL) techniques, contrasted against a baseline projection of an unlogged forest. Results from log and leave scenarios show that a stand logged according to Brazilian management requirements will require well over 120 years to recover its initial commercial volume, regardless of logging technique employed. Implementing RIL, however, accelerates this recovery. Scenarios imposing a 40-year cutting cycle raise the possibility of sustainable harvest volumes, although at significantly lower levels than is implied by current regulations. Meeting current Brazilian forest policy goals may require an increase in the planned total area of permanent production forest or the widespread adoption of silvicultural practices that increase stand recovery and volume accumulation rates after RIL harvests. Published by Elsevier B.V.

A Log-Linear Regression Model for the Beta-Weibull Distribution

We introduce the log-beta Weibull regression model based on the beta Weibull distribution (Famoye et al., 2005; Lee et al., 2007). We derive expansions for the moment generating function which do not depend on complicated functions. The new regression model represents a parametric family of models that includes as sub-models several widely known regression models that can be applied to censored survival data. We employ a frequentist analysis, a jackknife estimator, and a parametric bootstrap for the parameters of the proposed model. We derive the appropriate matrices for assessing local influences on the parameter estimates under different perturbation schemes and present some ways to assess global influences. Further, for different parameter settings, sample sizes, and censoring percentages, several simulations are performed. In addition, the empirical distribution of some modified residuals are displayed and compared with the standard normal distribution. These studies suggest that the residual analysis usually performed in normal linear regression models can be extended to a modified deviance residual in the proposed regression model applied to censored data. We define martingale and deviance residuals to evaluate the model assumptions. The extended regression model is very useful for the analysis of real data and could give more realistic fits than other special regression models.

Effect of Fusobacterium nucleatum on the T and B cell responses to Porphyromonas gingivalis in a mouse model

T cell cytokine profiles and specific serum antibody levels in five groups of BALB/c mice immunized with saline alone, viable Fusobacterium nucleatum ATCC 25586, viable Porphyromonas gingivalis ATCC 33277, F. nucleatum followed by P. gingivalis and P. gingivalis followed by F nucleatum were determined. Splenic CD4 and CD8 cells were examined for intracytoplasmic interleukin (IL)-4, interferon (IFN)-gamma and IL-10 by dual colour flow cytometry and the levels of serum anti-F. nucleatum and anti-P. gingivalis antibodies determined by an ELISA. Both Th1 and Th2 responses were demonstrated by all groups, and while there were slightly lower percentages of cytokine positive T cells in mice injected with F. nucleatum alone compared with the other groups immunized with bacteria., F nucleatum had no effect on the T cell production of cytokines induced by P gingivalis in the two groups immunized with both organisms. However, the percentages of cytokine positive CD8 cells were generally significantly higher than those of the CD4 cells. Mice immunized with F nucleatum alone had high levels of serum anti-E nucleatum antibodies with very low levels of P. gingivalis antibodies, whereas mice injected with P gingivalis alone produced anti-P. gingivalis antibodies predominantly. Although the levels of anti-E nucleatum antibodies in mice injected with E nucleatum followed by P. gingivalis were the same as in mice immunized with F nucleatum alone, antibody levels to P. gingivalis were very low. In contrast, mice injected with P. gingivalis followed by F nucleatum produced equal levels of both anti-P. gingivalis and anti-F nucleatum antibodies, although at lower levels than the other three groups immunized with bacteria, respectively. Anti-Actinobacillus actitiomycetemcomitans, Bacteroides forsythus and Prevotella intermedia serum antibody levels were also determined and found to be negligible. In conclusion, F nucleatum immunization does not affect the splenic T cell cytokine response to P. gingivalis. However, F nucleatum immunization prior to that of P. gingivalis almost completely inhibited the production of anti-P gingivalis antibodies while P. gingivalis injection before F. nucleatum demonstrated a partial inhibitory effect by P. gingivalis on antibody production to F. nucleatum. The significance of these results with respect to human periodontal disease is difficult to determine. However, they may explain in part differing responses to P. gingivalis in different individuals who may or may not have had prior exposure to F. nucleatum. Finally, the results suggested that P. gingivalis and F. nucleatum do not induce the production of cross-reactive antibodies to other oral microorganisms.

A zero-augmented gamma mixed model for longitudinal data with many zeros

In many occupational safety interventions, the objective is to reduce the injury incidence as well as the mean claims cost once injury has occurred. The claims cost data within a period typically contain a large proportion of zero observations (no claim). The distribution thus comprises a point mass at 0 mixed with a non-degenerate parametric component. Essentially, the likelihood function can be factorized into two orthogonal components. These two components relate respectively to the effect of covariates on the incidence of claims and the magnitude of claims, given that claims are made. Furthermore, the longitudinal nature of the intervention inherently imposes some correlation among the observations. This paper introduces a zero-augmented gamma random effects model for analysing longitudinal data with many zeros. Adopting the generalized linear mixed model (GLMM) approach reduces the original problem to the fitting of two independent GLMMs. The method is applied to evaluate the effectiveness of a workplace risk assessment teams program, trialled within the cleaning services of a Western Australian public hospital.

Robust model-order reduction of complex biological processes

This paper addresses robust model-order reduction of a high dimensional nonlinear partial differential equation (PDE) model of a complex biological process. Based on a nonlinear, distributed parameter model of the same process which was validated against experimental data of an existing, pilot-scale BNR activated sludge plant, we developed a state-space model with 154 state variables in this work. A general algorithm for robustly reducing the nonlinear PDE model is presented and based on an investigation of five state-of-the-art model-order reduction techniques, we are able to reduce the original model to a model with only 30 states without incurring pronounced modelling errors. The Singular perturbation approximation balanced truncating technique is found to give the lowest modelling errors in low frequency ranges and hence is deemed most suitable for controller design and other real-time applications. (C) 2002 Elsevier Science Ltd. All rights reserved.

A mechanistic model for carbon dioxide corrosion of mild steel in the presence of protective iron carbonate films - Part 3: Film growth model

A model of iron carbonate (FeCO3) film growth is proposed, which is an extension of the recent mechanistic model of carbon dioxide (CO2) corrosion by Nesic, et al. In the present model, the film growth occurs by precipitation of iron carbonate once saturation is exceeded. The kinetics of precipitation is dependent on temperature and local species concentrations that are calculated by solving the coupled species transport equations. Precipitation tends to build up a layer of FeCO3 on the surface of the steel and reduce the corrosion rate. On the other hand, the corrosion process induces voids under the precipitated film, thus increasing the porosity and leading to a higher corrosion rate. Depending on the environmental parameters such as temperature, pH, CO2 partial pressure, velocity, etc., the balance of the two processes can lead to a variety of outcomes. Very protective films and low corrosion rates are predicted at high pH, temperature, CO2 partial pressure, and Fe2+ ion concentration due to formation of dense protective films as expected. The model has been successfully calibrated against limited experimental data. Parametric testing of the model has been done to gain insight into the effect of various environmental parameters on iron carbonate film formation. The trends shown in the predictions agreed well with the general understanding of the CO2 corrosion process in the presence of iron carbonate films. The present model confirms that the concept of scaling tendency is a good tool for predicting the likelihood of protective iron carbonate film formation.

O caráter político-pedagógico dos movimentos populares de bairro da Grande São Pedro: avanços e recuos sob o imperativo da ordem capitalista

Este trabalho tem como objeto de estudo as ações organizativas dos movimentos populares de bairro, enquanto práticas político-pedagógicas. Tomamos como foco, as associações de moradores da região da Grande São Pedro. Apesar de ter ficado conhecida na década de 1980 pela situação de miséria, os moradores dessa região, historicamente perpassada pelo fenômeno da segregação socioespacial, encontraram nas adversidades motivação para a organização do movimento popular como forma de construir sua história e afirmar sua cidadania. Totalmente transformada no que tange à sua urbanização, a região ainda hoje apresenta um cenário adverso para os moradores. Nesse sentido, a importância da organização dos moradores na atualidade é fundamental para lutar contra as situações de opressão que se impõem sobre os mesmos. Entretanto, o quadro que os atuais movimentos populares de bairro desta região apresenta é de reprodução de um modelo político-cultural marcado pelo individualismo, com traços peculiares da formação social brasileira - caracterizada por práticas de centralização, dependência e clientelismo político. Deve-se registrar que apesar de também trazerem traços de lutas e resistência, a forma como atualmente acontecem, com ações em níveis imediatos, esvaziadas de conteúdo político mais amplo, sem articulação com movimentos mais abrangentes, acabam se expressando em um “associativismo individualizado”. Desta feita, reiteramos neste trabalho a necessidade de a classe trabalhadora brasileira retomar, reconstruir espaços que contribuam com a formação de lideranças, com a qualificação das bases desses movimentos, para que seus protagonistas possam consolidar uma prática político-pedagógica fundamentada na educação popular e com isso venham adensar as lutas da classe trabalhadora e somar ao projeto de construção da contra-hegemonia, visando à transformação social. Buscar-se-ia neste sentido, a consolidação de um projeto social mais igualitário, justo e verdadeiramente democrático, no qual seja possível a emancipação humana.

Coherent forecasting of multiple-decrement life tables: a test using Japanese cause of death data

Planners in public and private institutions would like coherent forecasts of the components of age-specic mortality, such as causes of death. This has been di cult toachieve because the relative values of the forecast components often fail to behave ina way that is coherent with historical experience. In addition, when the group forecasts are combined the result is often incompatible with an all-groups forecast. It hasbeen shown that cause-specic mortality forecasts are pessimistic when compared withall-cause forecasts (Wilmoth, 1995). This paper abandons the conventional approachof using log mortality rates and forecasts the density of deaths in the life table. Sincethese values obey a unit sum constraint for both conventional single-decrement life tables (only one absorbing state) and multiple-decrement tables (more than one absorbingstate), they are intrinsically relative rather than absolute values across decrements aswell as ages. Using the methods of Compositional Data Analysis pioneered by Aitchison(1986), death densities are transformed into the real space so that the full range of multivariate statistics can be applied, then back-transformed to positive values so that theunit sum constraint is honoured. The structure of the best-known, single-decrementmortality-rate forecasting model, devised by Lee and Carter (1992), is expressed incompositional form and the results from the two models are compared. The compositional model is extended to a multiple-decrement form and used to forecast mortalityby cause of death for Japan

An alternative method for dating unknown tephras based on a segmented regression model

In CoDaWork’05, we presented an application of discriminant function analysis (DFA) to 4 differentcompositional datasets and modelled the first canonical variable using a segmented regression modelsolely based on an observation about the scatter plots. In this paper, multiple linear regressions areapplied to different datasets to confirm the validity of our proposed model. In addition to dating theunknown tephras by calibration as discussed previously, another method of mapping the unknown tephrasinto samples of the reference set or missing samples in between consecutive reference samples isproposed. The application of these methodologies is demonstrated with both simulated and real datasets.This new proposed methodology provides an alternative, more acceptable approach for geologists as theirfocus is on mapping the unknown tephra with relevant eruptive events rather than estimating the age ofunknown tephra.Kew words: Tephrochronology; Segmented regression