RB Regulates DNA Double Strand Break Repair Pathway Choice by Mediating CtIP Dependent End Resection

Inactivation of the retinoblastoma tumor suppressor gene (RB1) leads to genome instability, and can be detected in retinoblastoma and other cancers. One damaging effect is causing DNA double strand breaks (DSB), which, however, can be repaired by homologous recombination (HR), classical non-homologous end joining (C-NHEJ), and micro-homology mediated end joining (MMEJ). We aimed to study the mechanistic roles of RB in regulating multiple DSB repair pathways. Here we show that HR and C-NHEJ are decreased, but MMEJ is elevated in RB-depleted cells. After inducing DSB by camptothecin, RB co-localizes with CtIP, which regulates DSB end resection. RB depletion leads to less RPA and native BrdU foci, which implies less end resection. In RB-depleted cells, less CtIP foci, and a lack of phosphorylation on CtIP Thr847, are observed. According to the synthetic lethality principle, based on the altered DSB repair pathway choice, after inducing DSBs by camptothecin, RB depleted cells are more sensitive to co-treatment with camptothecin and MMEJ blocker poly-ADP ribose polymerase 1 (PARP1) inhibitor. We propose a model whereby RB can regulate DSB repair pathway choice by mediating the CtIP dependent DNA end resection. The use of PARP1 inhibitor could potentially improve treatment outcomes for RB-deficient cancers.     

Micro-particle transport and deposition in a human oral airway model

Laminar-to-turbulent air flow for typical inhalation modes as well as micro-particle transport and wall deposition in a representative human oral airway model have been simulated using a commercial finite-volume code with user-enhanced programs. The computer model has been validated with experimental airflow and particle deposition data sets. For the first time, accurate local and segmentally averaged particle deposition fractions have been computed under transitional and turbulent flow conditions. Specifically, turbulence that occurs after the constriction in the oral airways for moderate and high-level breathing can enhance particle deposition in the trachea near the larynx, but it is more likely to affect the deposition of smaller particles, say, St<0.05. Particles released around the top/bottom zone of the inlet plane more easily deposit on the curved oral airway surface. Although more complicated geometric features of the oral airway may have a measurable effect on particle deposition, the present simulations with a relatively simple geometry exhibit the main features of laminar-transitional-turbulent particle suspension flows in actual human oral airways. Hence, the present model may serve as the “entryway” for simulating and analyzing airflow and particle deposition in the lung.     

Computational Models for Simulating Multicomponent Aerosol Evaporation in the Upper Respiratory Airways

An effective model for predicting multicomponent aerosol evaporation in the upper respiratory system that is capable of estimating the vaporization of individual components is needed for accurate dosimetry and toxicology analyses. In this study, the performance of evaporation models for multicomponent droplets over a range of volatilities is evaluated based on comparisons to available experimental results for conditions similar to aerosols in the upper respiratory tract. Models considered include a semiempirical correlation approach as well as resolved-volume computational simulations of single and multicomponent aerosol evaporations to test the effects of variable gas-phase properties, surface blowing velocity, and internal droplet temperature gradients. Of the parameters assessed, concentration-dependent gas-phase specific heat had the largest effect on evaporation and should be taken into consideration for respiratory aerosols that contain high volatility species, such as n-heptane, at significant concentrations. For heavier droplet components or conditions below body temperatures, semiempirical estimates were shown to be appropriate for respiratory aerosol conditions. In order to reduce the number of equations and properties required for complex mixtures, a resolved-volume evaporation model was used to identify a twelve-component surrogate representation of potentially toxic JP-8 fuel based on comparisons to experimentally reported droplet evaporation data. Due to the relatively slow evaporation rate of JP-8 aerosols, results indicate that a semiempirical evaporation model in conjunction with the identified surrogate mixture provide a computationally efficient method for computing droplet evaporation that can track individual toxic markers. However, semiempirical methodologies are in need of further development to effectively compute the evaporation of other higher volatility aerosols for which variable gas-phase specific heat does play a significant role.     

Modelling of long-term diffusion–reaction in a bentonite barrier for radioactive waste confinement

Bentonites have been proposed as buffer material for barriers in geological disposal facilities for radioactive waste. This material is expected to fill up by swelling the void between the canisters containing the waste and the surrounding ground. However, the bentonite barriers may be submitted to changes of humidity, temperature variation, fluid interaction, mass transport, etc. This could modify the physico-chemical performance of the barrier, mainly on the interface with the steel container and with the geological barrier. The engineered barrier development necessitates thus the study of the physico-chemical stability of its mineral component as a function of time under the conditions of the repository in the long-term.The purpose of the present study was two-fold. Firstly, it was hoped to simulate the chemical transformations (geochemical and cation exchange reactions) coupled with diffusion of chemical-elements into the engineered barrier under repository conditions by applying a thermokinetic hydrochemical code (KIRMAT: Kinetic Reactions and Mass transport).Secondly, it was hoped to apply a simplified method to estimate the swelling capacity evolution by a volume balance in the fluid-saturated engineered barrier, considering that the decay of swelling capacity is directly proportional on the volume of transformed montmorillonite and, taking into account that it may be partially compensated by the volume of neo-formed swelling clays.The system modelled herein was considered to consist of 1-m thick zone of water-saturated engineered barrier. This non-equilibrated system was placed in contact with a geological fluid on one side, which was then allowed to diffuse into the barrier, while the other side was kept in contact with a source of metallic iron. Reducing initial conditions(P_O2 0; Eh = − 200 mV) and a constant reaction temperature (100 °C) were considered.The results showed that the EB in contact with the geological fluid was highly transformed after 10,000 years, whereas the most significant chemical processes were illitization, cation exchange and saponization, extending up to 20 cm into the EB. Chemical transformations of minor importance in the EB were identified as well, such as a neo-formation of silicates (quartz, cristobalite), anhydrite, laumontite, magnetite and chlorite in the system.A simplified method based on volume balance showed that the swelling capacity of the bentonite barrier is slightly affected after 10,000 years of diffusion–reaction (D close to 1) because the volume of neo-formed swelling-clays is almost directly proportional to the volume of transformed Na/Ca-montmorillonite, except for a strong illitization and/or neo-formation of non-swelling clays. In the present study, this simple approach predicted that the decay of swelling capacity of the engineered barrier is drastically affected close to the geological barrier-engineered barrier interface. Out this zone the swelling capacity decay lies between 5% and 11%.     

3D modelling of Ti–6Al–4V linear friction welds

Linear friction welding (LFW) is a solid-state joining process that significantly reduces manufacturing costs when fabricating Ti–6Al–4V aircraft components. This article describes the development of a novel 3D LFW process model for joining Ti–6Al–4V. Displacement histories were taken from experiments and used as modelling inputs; herein is the novelty of the approach, which resulted in decreased computational time and memory storage requirements. In general, the models captured the experimental weld phenomena and showed that the thermo-mechanically affected zone and interface temperature are reduced when the workpieces are oscillated along the shorter of the two interface contact dimensions. Moreover, the models showed that unbonded regions occur at the corners of the weld interface, which are eliminated by increasing the burn-off.     

Comparison of analytical and CFD models with regard to micron particle deposition in a human 16-generation tracheobronchial airway model

A representative human tracheobronchial tree has been geometrically represented with adjustable triple-bifurcation units (TBUs) in order to effectively simulate local and global micron particle depositions. It is the first comprehensive attempt to compute micron-particle transport in a (Weibel Type A) 16-generation model with realistic inlet conditions. The CFD modeling predictions are compared to experimental observations as well as analytical modeling results. Based on the findings with the validated computer simulation model, the following conclusions can be drawn:(i) Surprisingly, simulated inspiratory deposition fractions for the entire tracheobronchial region (say, G0–G15) with repeated TBUs in parallel and in series agree rather well with those calculated using analytical/semi-empirical expressions. However, the predicted particle-deposition fractions based on such analytical formulas differ greatly from the present simulation results for most local bifurcations, due to the effects of local geometry and resulting local flow features and particle distributions. Clearly, the effects of realistic geometries, flow structures and particle distributions in different individual bifurcations accidentally cancel each other so that the simulated deposition efficiencies during inspiration in a relatively large airway region may agree quite well with those obtained from analytical expressions. Furthermore, with the lack of local resolution, analytical models do not provide any physical insight to the air–particle dynamics in the tracheobronchial region.(ii) The maximum deposition enhancement factors (DEF) may be in the order of 10² to 10³ for micron particles in the tracheobronchial airways, implying potential health effects when the inhaled particles are toxic.(iii) The presence of sedimentation for micron particles in lower bronchial airways may change the local impaction-based deposition patterns seen for larger airways and hence reduces the maximum DEF values.(iv) Rotation of an airway bifurcation cause a significant impact on distal bifurcations rather than on the proximal ones. Such geometric effects are minor when compared to the effects of airflow and particle transport/deposition history, i.e., upstream effects.     

Creating a reusable GUI component

Application development of a large number of graphical user interface (GUI) screens and reports requires a labor‐intensive process. In the typical scenario, a GUI developer drags each component, such as the textfield, label, and error messages, on each of the new GUI screens or reports. They then set the component properties and perhaps write any validation routines for input data. Using the proposed Observation Panel Bean (OPB), the developer drags only one component per field, and the OPB dynamically builds the GUI components with consistent properties and links the observation field to the needed validation routine. With little development effort these fields are simply selected from the data dictionary and placed on the GUI. The proposed OPB uses Fowler's observation pattern as a high‐level abstraction representing attributes observed about information in the application domain. The panel collaborates with the observation pattern to set the label, error message, and properties of the various components. Yoder's validator pattern collaborates with the observation pattern and the data dictionary to validate the observations. The proposed OPB decreases GUI development time, adds adaptability to GUI design, and increases consistency in GUI component presentation. Copyright © 2002 John Wiley & Sons, Ltd.     

Two-site enzyme immunometric assays for determination of native and denatured beta-lactoglobulin

Two enzyme immunometric assays suitable for measuring native and denatured beta-lactoglobulin (BLg) have been developed. The assays were performed in 96-well microtitre plates and were based on the use of pairs of monoclonal antibodies specific to either the native form or the reduced and carboxymethylated form of BLg (RCM-BLg). Detection limits of 30 and 200 pg/ml were obtained for the native BLg and the RCM-BLg assay, respectively, with very low or negligible cross-reactivity of the other milk proteins and tryptic fragments of BLg. The validity of the assays in different media such as cow's milk and cow's milk products, saline buffer or serum was supported by recovery experiments. The assays were first applied to the determination of BLg and RCM-BLg in PBS and in raw skimmed milk. The ability of the RCM-BLg assay to detect heat-denatured BLg was confirmed by a kinetic study of BLg heat-denaturation in the two media. During heat treatment, the decrease in the concentration of native BLg was associated with an increase in denatured BLg specifically detected by the RCM-BLg assay. By selecting an appropriate monoclonal antibody which failed to recognize caprine BLg, we were able to establish a modified sandwich immunoassay permitting very sensitive detection of cow's milk in goat's milk.     

Mullerian adenosarcoma of the uterine corpus associated with tamoxifen therapy: a report of six cases and a review of tamoxifen-associated endometrial lesions

Six consultation cases of mullerian adenosarcoma of the uterus were encountered in women who were receiving adjuvant tamoxifen therapy for carcinoma of the breast. To our knowledge, only one previous similar case has been reported. The women, who were 48-76 years of age, had received tamoxifen for periods of 6 months to 4 years (mean 2.7 years) in five of the cases; the duration of tamoxifen therapy in the sixth case is unknown. All of the tumors were polypoid endometrial masses that superficially invaded the myometrium in two cases. The microscopic appearance of the tumors was similar to that of previously described uterine mullerian adenosarcomas. These and other recent observations indicate that tamoxifen treatment may be complicated by uterine neoplasms other than endometrial adenocarcinoma. These findings also support previous observations that prolonged exogenous or endogenous hyperestrinism may lead to the development of mesenchymal and mixed epithelial-mesenchymal tumors of the uterus.