Coordinated activation of candidate proto-oncogenes and cancer testes antigens via promoter demethylation in head and neck cancer and lung cancer.

BACKGROUND: Epigenetic alterations have been implicated in the pathogenesis of solid tumors, however, proto-oncogenes activated by promoter demethylation have been sporadically reported. We used an integrative method to analyze expression in primary head and neck squamous cell carcinoma (HNSCC) and pharmacologically demethylated cell lines to identify aberrantly demethylated and expressed candidate proto-oncogenes and cancer testes antigens in HNSCC. METHODOLOGY/PRINCIPAL FINDINGS: We noted coordinated promoter demethylation and simultaneous transcriptional upregulation of proto-oncogene candidates with promoter homology, and phylogenetic footprinting of these promoters demonstrated potential recognition sites for the transcription factor BORIS. Aberrant BORIS expression correlated with upregulation of candidate proto-oncogenes in multiple human malignancies including primary non-small cell lung cancers and HNSCC, induced coordinated proto-oncogene specific promoter demethylation and expression in non-tumorigenic cells, and transformed NIH3T3 cells. CONCLUSIONS/SIGNIFICANCE: Coordinated, epigenetic unmasking of multiple genes with growth promoting activity occurs in aerodigestive cancers, and BORIS is implicated in the coordinated promoter demethylation and reactivation of epigenetically silenced genes in human cancers.

Pseudomonas aeruginosa vesicles associate with and are internalized by human lung epithelial cells.

BACKGROUND: Pseudomonas aeruginosa is the major pathogen associated with chronic and ultimately fatal lung infections in patients with cystic fibrosis (CF). To investigate how P. aeruginosa-derived vesicles may contribute to lung disease, we explored their ability to associate with human lung cells. RESULTS: Purified vesicles associated with lung cells and were internalized in a time- and dose-dependent manner. Vesicles from a CF isolate exhibited a 3- to 4-fold greater association with lung cells than vesicles from the lab strain PAO1. Vesicle internalization was temperature-dependent and was inhibited by hypertonic sucrose and cyclodextrins. Surface-bound vesicles rarely colocalized with clathrin. Internalized vesicles colocalized with the endoplasmic reticulum (ER) marker, TRAPalpha, as well as with ER-localized pools of cholera toxin and transferrin. CF isolates of P. aeruginosa abundantly secrete PaAP (PA2939), an aminopeptidase that associates with the surface of vesicles. Vesicles from a PaAP knockout strain exhibited a 40% decrease in cell association. Likewise, vesicles from PAO1 overexpressing PaAP displayed a significant increase in cell association. CONCLUSION: These data reveal that PaAP promotes the association of vesicles with lung cells. Taken together, these results suggest that P. aeruginosa vesicles can interact with and be internalized by lung epithelial cells and contribute to the inflammatory response during infection.

Interrogation of individual intratumoral B lymphocytes from lung cancer patients for molecular target discovery.

Intratumoral B lymphocytes are an integral part of the lung tumor microenvironment. Interrogation of the antibodies they express may improve our understanding of the host response to cancer and could be useful in elucidating novel molecular targets. We used two strategies to explore the repertoire of intratumoral B cell antibodies. First, we cloned VH and VL genes from single intratumoral B lymphocytes isolated from one lung tumor, expressed the genes as recombinant mAbs, and used the mAbs to identify the cognate tumor antigens. The Igs derived from intratumoral B cells demonstrated class switching, with a mean VH mutation frequency of 4%. Although there was no evidence for clonal expansion, these data are consistent with antigen-driven somatic hypermutation. Individual recombinant antibodies were polyreactive, although one clone demonstrated preferential immunoreactivity with tropomyosin 4 (TPM4). We found that higher levels of TPM4 antibodies were more common in cancer patients, but measurement of TPM4 antibody levels was not a sensitive test for detecting cancer. Second, in an effort to focus our recombinant antibody expression efforts on those B cells that displayed evidence of clonal expansion driven by antigen stimulation, we performed deep sequencing of the Ig genes of B cells collected from seven different tumors. Deep sequencing demonstrated somatic hypermutation but no dominant clones. These strategies may be useful for the study of B cell antibody expression, although identification of a dominant clone and unique therapeutic targets may require extensive investigation.

Two Cases of Late Shone Syndrome With Pulmonary Hypertension: Heart-Lung Transplant or Valve Surgery?

Two cases of Shone syndrome with severe mitral and aortic valve problems and pulmonary hypertension were referred for heart-lung transplantation. Severely elevated pulmonary vascular resistance (PVR) was confirmed as was severe periprosthetic mitral and aortic regurgitation. Based on the severity of the valve lesions in both patients, surgery was decided upon and undertaken. Both experienced early pulmonary hypertensive crises, one more than the other, that gradually subsided, followed by excellent recovery and reversal of pulmonary hypertension and PVR. These cases illustrate Braunwald's concept that pulmonary hypertension secondary to left-sided valve disease is reversible.

The prediction of fire propagation in enclosure fires

In this paper we present some early work concerned with the development of a simple solid fuel combustion model incorporated within a Computational Fluid Dynamics (CFD) framework. The model is intended for use in engineering applications of fire field modelling and represents an extension of this technique to situations involving the combustion of solid cellulosic hels A simple solid &el combustion model consisting of a thermal pyrolysis model, a six flux radiation model and an eddydissipation model for gaseous combustion have been developed and implemented within the CFD code CFDS-FLOW3D The model is briefly described and demonstrated through two applications involving fire spread in a compartment with a plywood lined ceiling. The two scenarios considered involve a fire in an open and closed compartment The model is shown to be able to qualitatively predict behaviours similar to flashover - in the case of the open room - and backdrafl - in the case of the initially closed room.

The FUELCON meta-architecture, II: alternatives for parameter prediction

We continue the discussion of the decision points in the FUELCON metaarchitecture. Having discussed the relation of the original expert system to its sequel projects in terms of an AND/OR tree, we consider one further domain for a neural component: parameter prediction downstream of the core reload candidate pattern generator, thus, a replacement for the NOXER simulator currently in use in the project.

The numerical simulation of noncharring thermal degradation and its application to the prediction of compartment fire development

In this paper we present some work concerned with the development and testing of a simple solid fuel combustion model incorporated within a Computational Fluid Dynamics (CFD) framework. The model is intended for use in engineering applications of fire field modeling and represents an extension of this technique to situations involving the combustion of solid fuels. The CFD model is coupled with a simple thermal pyrolysis model for combustible solid noncharring fuels, a six-flux radiation model and an eddy-dissipation model for gaseous combustion. The model is then used to simulate a series of small-scale room fire experiments in which the target solid fuel is polymethylmethacrylate. The numerical predictions produced by this coupled model are found to be in very good agreement with experimental data. Furthermore, numerical predictions of the relationship between the air entrained into the fire compartment and the ventilation factor produce a characteristic linear correlation with constant of proportionality 0.38 kg/sm5/12. The simulation results also suggest that the model is capable of predicting the onset of "flashover" type behavior within the fire compartment.

A computational model for defect prediction in shape castings based on the interaction of free surface flow, heat transfer, and solidification phenomena

High-integrity castings require sophisticated design and manufacturing procedures to ensure they are essentially macrodefect free. Unfortunately, an important class of such defects—macroporosity, misruns, and pipe shrinkage—are all functions of the interactions of free surface flow, heat transfer, and solidication in complex geometries. Because these defects arise as an interaction of the preceding continuum phenomena, genuinely predictive models of these defects must represent these interactions explicitly. This work describes an attempt to model the formation of macrodefects explicitly as a function of the interacting continuum phenomena in arbitrarily complex three-dimensional geometries. The computational approach exploits a compatible set of finite volume procedures extended to unstructured meshes. The implementation of the model is described together with its testing and a measure of validation. The model demonstrates the potential to predict reliably shrinkage macroporosity, misruns, and pipe shrinkage directly as a result of interactions among free-surface fluid flow, heat transfer, and solidification.

Computational model for prediction of particle degradation during dilute phase pneumatic conveying: the use of a laboratory scale degradation tester for the determination of degradation propensity

The overall objective of this work is to develop a computational model of particle degradation during dilute-phasepneumatic conveying. A key feature of such a model is the prediction of particle breakage due to particle–wall collisions in pipeline bends. This paper presents a method for calculating particle impact degradation propensity under a range of particle velocities and particle sizes. It is based on interpolation on impact data obtained in a new laboratory-scale degradation tester. The method is tested and validated against experimental results for degradation at 90± impact angle of a full-size distribution sample of granulated sugar. In a subsequent work, the calculation of degradation propensity is coupled with a ow model of the solids and gas phases in the pipeline.

Computational model for prediction of particle degradation during dilute-phase pneumatic conveying: modeling of dilute-phase pneumatic conveying

A complete model of particle impact degradation during dilute-phase pneumatic conveying is developed, which combines a degradation model, based on the experimental determination of breakage matrices, and a physical model of solids and gas flow in the pipeline. The solids flow in a straight pipe element is represented by a model consisting of two zones: a strand-type flow zone immediately downstream of a bend, followed by a fully suspended flow region after dispersion of the strand. The breakage matrices constructed from data on 90° angle single-impact tests are shown to give a good representation of the degradation occurring in a pipe bend of 90° angle. Numerical results are presented for degradation of granulated sugar in a large scale pneumatic conveyor.

Solder life prediction in a thermal analysis software environment

This paper describes recent developments made to the stress analysis module within FLOTHERM, extending its capability to handle viscoplastic behavior. It also presents the validation of this approach and results obtained for an SMT resistor as an illustrative example. Lifetime predictions are made using the creep strain energy based models of Darveaux. Comment is made about the applicability of the damage model to the geometry of the joint under study.

Support vector machines for regression and applications to software quality prediction

Software metrics are the key tool in software quality management. In this paper, we propose to use support vector machines for regression applied to software metrics to predict software quality. In experiments we compare this method with other regression techniques such as Multivariate Linear Regression, Conjunctive Rule and Locally Weighted Regression. Results on benchmark dataset MIS, using mean absolute error, and correlation coefficient as regression performance measures, indicate that support vector machines regression is a promising technique for software quality prediction. In addition, our investigation of PCA based metrics extraction shows that using the first few Principal Components (PC) we can still get relatively good performance.

Lifetime prediction for power electronics module substrate mount-down solder interconnect

A numerical modeling method for the prediction of the lifetime of solder joints of relatively large solder area under cyclic thermal-mechanical loading conditions has been developed. The method is based on the Miner's linear damage accumulation rule and the properties of the accumulated plastic strain in front of the crack in large area solder joint. The nonlinear distribution of the damage indicator in the solder joints have been taken into account. The method has been used to calculate the lifetime of the solder interconnect in a power module under mixed cyclic loading conditions found in railway traction control applications. The results show that the solder thickness is a parameter that has a strong influence on the damage and therefore the lifetime of the solder joint while the substrate width and the thickness of the baseplate are much less important for the lifetime