Computational Verification of Two Universal Relations for Simple Ionic Liquids. Kinetic Properties of a Model 2:1 Molten Salt

Two semianalytical relations [Nature, 1996, 381, 137 and Phys. Rev. Lett. 2001, 87, 245901] predicting dynamical coefficients of simple liquids on the basis of structural properties have been tested by extensive molecular dynamics simulations for an idealized 2:1 model molten salt. In agreement with previous simulation studies, our results support the validity of the relation expressing the self-diffusion coefficient as a Function of the radial distribution functions for all thermodynamic conditions such that the system is in the ionic (ie., fully dissociated) liquid state. Deviations are apparent for high-density samples in the amorphous state and in the low-density, low-temperature range, when ions condense into AB(2) molecules. A similar relation predicting the ionic conductivity is only partially validated by our data. The simulation results, covering 210 distinct thermodynamic states, represent an extended database to tune and validate semianalytical theories of dynamical properties and provide a baseline for the interpretation of properties of more complex systems such as the room-temperature ionic liquids.

Verification of McCabe's Delta L Law for Growth of Lysozyme Crystals by Hanging Drop Method

Lysozyme is a naturally occurring enzyme in egg white and has high commercial importance due to its antimicrobial properties. The main objective of this work was to study the growth rate of lysozyme crystals isolated from egg for the first 72 hours and verify the results with McCabe’s constant crystal growth theory. Hanging drop crystallization method was used to form high purity lysozyme crystals from the embryonic stage. To this end, this work differs from an earlier work of Forsythe et al., who used seed crystals in the size range of 10 µm - 40 µm for face growth measurements at different pH values. The maximum crystal size recorded in the present work was 392.86 µm, which is within the typical size range of 50 µm - 500 µm for which constant crystal growth is expected to hold according to McCabe’s ?L law. Electron micrographs (SEM) revealed the structure and dimensions of the crystals while SDS-Page was used to measure the purity of the crystals. The SEM results showed that that lysozyme growth rate was linear and agreed with McCabe’s constant growth theory, producing a growth rate of 1.77 x 10-3 µm .s-1

Large Scale Verification of MPI Programs Using Lamport Clocks with Lazy Update

We propose a dynamic verification approach for large-scale message passing programs to locate correctness bugs caused by unforeseen nondeterministic interactions. This approach hinges on an efficient protocol to track the causality between nondeterministic message receive operations and potentially matching send operations. We show that causality tracking protocols that rely solely on logical clocks fail to capture all nuances of MPI program behavior, including the variety of ways in which nonblocking calls can complete. Our approach is hinged on formally defining the matches-before relation underlying the MPI standard, and devising lazy update logical clock based algorithms that can correctly discover all potential outcomes of nondeterministic receives in practice. can achieve the same coverage as a vector clock based algorithm while maintaining good scalability. LLCP allows us to analyze realistic MPI programs involving a thousand MPI processes, incurring only modest overheads in terms of communication bandwidth, latency, and memory consumption. © 2011 IEEE.

JMJD6 is a driver of cellular proliferation and motility and a marker of poor prognosis in breast cancer

We developed an analytic strategy that correlates gene expression and clinical outcomes as a means to identify novel candidate oncogenes operative in breast cancer. This analysis, followed by functional characterization, resulted in the identification of Jumonji Domain Containing 6 (JMJD6) protein as a novel driver of oncogenic properties in breast cancer.

Preparation of planar retinal specimens:verification by histology, mRNA profiling, and proteome analysis

Elucidation of the transcriptome and proteome of the normal retina will be difficult since it is comprised of at least 55 different cell types. However the characteristic layered cellular anatomy of the retina makes it amenable to planar sectioning, enabling the generation of enriched retinal cell populations. The aim of this study was to validate a reproducible method for preparing enriched retinal layers from porcine retina.

Impact of oncogenic driver mutations on feedback between the PI3K and MEK pathways in cancer cells

Inhibition of the PI3K (phosphoinositide 3-kinase)/Akt/mTORC1 (mammalian target of rapamycin complex 1) and Ras/MEK [MAPK (mitogen-activated protein kinase)/ERK (extracellular-signal-regulated kinase) kinase]/ERK pathways for cancer therapy has been pursued for over a decade with limited success. Emerging data have indicated that only discrete subsets of cancer patients have favourable responses to these inhibitors. This is due to genetic mutations that confer drug insensitivity and compensatory mechanisms. Therefore understanding of the feedback mechanisms that occur with respect to specific genetic mutations may aid identification of novel biomarkers that predict patient response. In the present paper, we show that feedback between the PI3K/Akt/mTORC1 and Ras/MEK/ERK pathways is cell-line-specific and highly dependent on the activating mutation of K-Ras or overexpression c-Met. We found that cell lines exhibited differential signalling and apoptotic responses to PD184352, a specific MEK inhibitor, and PI103, a second-generation class I PI3K inhibitor. We reveal that feedback from the PI3K/Akt/mTORC1 to the Ras/MEK/ERK pathway is present in cancer cells harbouring either K-Ras activating mutations or amplification of c-Met but not the wild-type counterparts. Moreover, we demonstrate that inhibition of protein phosphatase activity by OA (okadaic acid) restored PI103-mediated feedback in wild-type cells. Together, our results demonstrate a novel mechanism for feedback between the PI3K/Akt/mTORC1 and the Ras/MEK/ERK pathways that only occurs in K-Ras mutant and c-Met amplified cells but not the isogenic wild-type cells through a mechanism that may involve inhibition of a specific endogenous phosphatase(s) activity. We conclude that monitoring K-Ras and c-Met status are important biomarkers for determining the efficacy of PI103 and other PI3K/Akt inhibitors in cancer therapy.

Implementation of phantom-less IMRT delivery verification using Varian DynaLog files and R/V output

This study aims to evaluate the use of Varian radiotherapy dynamic treatment log (DynaLog) files to verify IMRT plan delivery as part of a routine quality assurance procedure. Delivery accuracy in terms of machine performance was quantified by multileaf collimator (MLC) position errors and fluence delivery accuracy for patients receiving intensity modulated radiation therapy (IMRT) treatment. The relationship between machine performance and plan complexity, quantified by the modulation complexity score (MCS) was also investigated. Actual MLC positions and delivered fraction of monitor units (MU), recorded every 50 ms during IMRT delivery, were extracted from the DynaLog files. The planned MLC positions and fractional MU were taken from the record and verify system MLC control file. Planned and delivered beam data were compared to determine leaf position errors with and without the overshoot effect. Analysis was also performed on planned and actual fluence maps reconstructed from the MLC control file and delivered treatment log files respectively. This analysis was performed for all treatment fractions for 5 prostate, 5 prostate and pelvic node (PPN) and 5 head and neck (H&N) IMRT plans, totalling 82 IMRT fields in ∼5500 DynaLog files. The root mean square (RMS) leaf position errors without the overshoot effect were 0.09, 0.26, 0.19 mm for the prostate, PPN and H&N plans respectively, which increased to 0.30, 0.39 and 0.30 mm when the overshoot effect was considered. Average errors were not affected by the overshoot effect and were 0.05, 0.13 and 0.17 mm for prostate, PPN and H&N plans respectively. The percentage of pixels passing fluence map gamma analysis at 3%/3 mm was 99.94 ± 0.25%, which reduced to 91.62 ± 11.39% at 1%/1 mm criterion. Leaf position errors, but not gamma passing rate, were directly related to plan complexity as determined by the MCS. Site specific confidence intervals for average leaf position errors were set at -0.03-0.12 mm for prostate and -0.02-0.28 mm for more complex PPN and H&N plans. For all treatment sites confidence intervals for RMS errors with the overshoot was set at 0-0.50 mm and for the percentage of pixels passing a gamma analysis at 1%/1 mm a confidence interval of 68.83% was set also for all treatment sites. This work demonstrates the successful implementation of treatment log files to validate IMRT deliveries and how dynamic log files can diagnose delivery errors not possible with phantom based QC. Machine performance was found to be directly related to plan complexity but this is not the dominant determinant of delivery accuracy.

Multibody modelling of a TB31 and a TB32 crash test with vertical portable concrete barriers: model verification and sensitivity analysis.

In this article the multibody simulation software package MADYMO for analysing and optimizing occupant safety design was used to model crash tests for Normal Containment barriers in accordance with EN 1317. The verification process was carried out by simulating a TB31 and a TB32 crash test performed on vertical portable concrete barriers and by comparing the numerical results to those obtained experimentally. The same modelling approach was applied to both tests to evaluate the predictive capacity of the modelling at two different impact speeds. A sensitivity analysis of the vehicle stiffness was also carried out. The capacity to predict all of the principal EN1317 criteria was assessed for the first time: the acceleration severity index, the theoretical head impact velocity, the barrier working width and the vehicle exit box. Results showed a maximum error of 6% for the acceleration severity index and 21% for theoretical head impact velocity for the numerical simulation in comparison to the recorded data. The exit box position was predicted with a maximum error of 4°. For the working width, a large percentage difference was observed for test TB31 due to the small absolute value of the barrier deflection but the results were well within the limit value from the standard for both tests. The sensitivity analysis showed the robustness of the modelling with respect to contact stiffness increase of ±20% and ±40%. This is the first multibody model of portable concrete barriers that can reproduce not only the acceleration severity index but all the test criteria of EN 1317 and is therefore a valuable tool for new product development and for injury biomechanics research.

Investigation into the radiobiological consequences of pre-treatment verification imaging with megavoltage X-rays in radiotherapy

Objective: The aim of this study was to investigate the effect of pre-treatment verification imaging with megavoltage (MV) X-rays on cancer and normal cell survival in vitro and to compare the findings with theoretically modelled data. Since the dose received from pre-treatment imaging can be significant, incorporation of this dose at the planning stage of treatment has been suggested.

Methods: The impact of imaging dose incorporation on cell survival was investigated by clonogenic assay, irradiating DU-145 prostate cancer, H460 non-small cell lung cancer and AGO-1522b normal tissue fibroblast cells. Clinically relevant imaging-to-treatment times of 7.5 minutes and 15 minutes were chosen for this study. The theoretical magnitude of the loss of radiobiological efficacy due to sublethal damage repair was investigated using the Lea-Catcheside dose protraction factor model.

Results: For the cell lines investigated, the experimental data showed that imaging dose incorporation had no significant impact upon cell survival. These findings were in close agreement with the theoretical results.

Conclusions: For the conditions investigated, the results suggest that allowance for the imaging dose at the planning stage of treatment should not adversely affect treatment efficacy.

Advances in Knowledge: There is a paucity of data in the literature on imaging effects in radiotherapy. This paper presents a systematic study of imaging dose effects on cancer and normal cell survival, providing both theoretical and experimental evidence for clinically relevant imaging doses and imaging-to-treatment times. The data provide a firm foundation for further study into this highly relevant area of research.

Microstructural analysis of non-woven fabrics using scanning electron microscopy and image processing. Part 1:Development and verification of the methods

This paper reports image analysis methods that have been developed to study the microstructural changes of non-wovens made by the hydroentanglement process. The validity of the image processing techniques has been ascertained by applying them to test images with known properties. The parameters in preprocessing of the scanning electron microscope (SEM) images used in image processing have been tested and optimized. The fibre orientation distribution is estimated using fast Fourier transform (FFT) and Hough transform (HT) methods. The results obtained using these two methods are in good agreement. The HT method is more demanding in computational time compared with the Fourier transform (FT) method. However, the advantage of the HT method is that the actual orientation of the lines can be concluded directly from the result of the transform without the need for any further computation. The distribution of the length of the straight fibre segments of the fabrics is evaluated by the HT method. The effect of curl of the fibres on the result of this evaluation is shown.