Evaluation of Altered Kras Codon Bias and NOS Inhibition During Lung Tumorigenesis

The small GTPases HRAS, NRAS and KRAS are mutated in approximately one-third of all human cancers, rendering the proteins constitutively active and oncogenic. Lung cancer is the leading cause of cancer deaths worldwide, and more than 20% of human lung cancers harbor mutations in RAS, with 98% of those occurring in the KRAS isoform. While there have been many advances in the understanding of KRAS–driven lung tumorigenesis, it remains a therapeutic challenge. To further this understanding and assess novel approaches for treatment, I have investigated two aspects of Kras–driven tumorigenesis in the lung:

(I) Despite nearly identical protein sequences, the three RAS proto-oncogenes exhibit divergent codon usage. Of the three isoforms, KRAS contains the most rare codons resulting in lower levels of KRAS protein expression relative to HRAS and NRAS. To determine the consequences of rare codon bias during de novo tumorigenesis, we created a knock-in Krasex3op mouse in which synonymous mutations in exon 3 converted codons from rare to common. These mice had reduced tumor burden and fewer oncogenic mutations in the Krasex3op allele following carcinogen exposure. The reduction in tumorigenesis appeared to be a product of rare codons affecting both the oncogenic and non–oncogenic alleles. Converting rare codons to common codons yielded a more potent oncogenic allele that promoted growth arrest and enhanced tumor suppression by the non-oncogenic allele. Thus, rare codons play an integral role in Kras tumorigenesis.

(II) Lung cancer patients exhale higher levels of NO and iNOS-/- mice are resistant to chemically induced lung tumorigenesis. I hypothesize that NO promotes Kras–driven lung adenocarcinoma, and NOS inhibition may decrease Kras–driven lung tumorigenesis. To test this hypothesis, I assessed efficacy of the NOS inhibitor L–NAME in a genetically engineered mouse model of Kras-driven lung adenocarcinoma. Adenoviral Cre recombinase was delivered into the lungs intranasally, resulting in expression of oncogenic KrasG12D and dominant-negative Trp53R172H in lung epithelial cells. L–NAME treatment was provided in the water and continued until survival endpoints. In this model, L–NAME treatment decreased tumor growth and prolonged survival. These data establish a potential clinical role for NOS inhibition in lung cancer treatment.

Intravital microscopy evaluation of angiogenesis and its effects on glucose sensor performance.

An optical window model for the rodent dorsum was used to perform chronic and quantitative intravital microscopy and laser Doppler flowmetry of microvascular networks adjacent to functional and non-functional glucose sensors. The one-sided configuration afforded direct, real-time observation of the tissue response to bare (unmodified, smooth surface) sensors and sensors coated with porous poly-L-lactic acid (PLLA). Microvessel length density and red blood cell flux (blood perfusion) within 1 mm of the sensors were measured bi-weekly over 2 weeks. When non-functional sensors were fully implanted beneath the windows, the porous coated sensors had two-fold more vasculature and significantly higher blood perfusion than bare sensors on Day 14. When functional sensors were implanted percutaneously, as in clinical use, no differences in baseline current, neovascularization, or tissue perfusion were observed between bare and porous coated sensors. However, percutaneously implanted bare sensors had two-fold more vascularity than fully implanted bare sensors by Day 14, indicating the other factors, such as micromotion, might be stimulating angiogenesis. Despite increased angiogenesis adjacent to percutaneous sensors, modest sensor current attenuation occurred over 14 days, suggesting that factors other than angiogenesis may play a dominant role in determining sensor function.

Live Imaging of Host-Parasite Interactions in a Zebrafish Infection Model Reveals Cryptococcal Determinants of Virulence and Central Nervous System Invasion.

UNLABELLED: The human fungal pathogen Cryptococcus neoformans is capable of infecting a broad range of hosts, from invertebrates like amoebas and nematodes to standard vertebrate models such as mice and rabbits. Here we have taken advantage of a zebrafish model to investigate host-pathogen interactions of Cryptococcus with the zebrafish innate immune system, which shares a highly conserved framework with that of mammals. Through live-imaging observations and genetic knockdown, we establish that macrophages are the primary immune cells responsible for responding to and containing acute cryptococcal infections. By interrogating survival and cryptococcal burden following infection with a panel of Cryptococcus mutants, we find that virulence factors initially identified as important in causing disease in mice are also necessary for pathogenesis in zebrafish larvae. Live imaging of the cranial blood vessels of infected larvae reveals that C. neoformans is able to penetrate the zebrafish brain following intravenous infection. By studying a C. neoformans FNX1 gene mutant, we find that blood-brain barrier invasion is dependent on a known cryptococcal invasion-promoting pathway previously identified in a murine model of central nervous system invasion. The zebrafish-C. neoformans platform provides a visually and genetically accessible vertebrate model system for cryptococcal pathogenesis with many of the advantages of small invertebrates. This model is well suited for higher-throughput screening of mutants, mechanistic dissection of cryptococcal pathogenesis in live animals, and use in the evaluation of therapeutic agents. IMPORTANCE: Cryptococcus neoformans is an important opportunistic pathogen that is estimated to be responsible for more than 600,000 deaths worldwide annually. Existing mammalian models of cryptococcal pathogenesis are costly, and the analysis of important pathogenic processes such as meningitis is laborious and remains a challenge to visualize. Conversely, although invertebrate models of cryptococcal infection allow high-throughput assays, they fail to replicate the anatomical complexity found in vertebrates and, specifically, cryptococcal stages of disease. Here we have utilized larval zebrafish as a platform that overcomes many of these limitations. We demonstrate that the pathogenesis of C. neoformans infection in zebrafish involves factors identical to those in mammalian and invertebrate infections. We then utilize the live-imaging capacity of zebrafish larvae to follow the progression of cryptococcal infection in real time and establish a relevant model of the critical central nervous system infection phase of disease in a nonmammalian model.

Performance evaluation of the register insertion protocol for voice-data integration

The performance of the register insertion protocol for mixed voice-data traffic is investigated by simulation. The simulation model incorporates a common insertion buffer for station and ring packets. Bandwidth allocation is achieved by imposing a queue limit at each node. A simple priority scheme is introduced by allowing the queue limit to vary from node to node. This enables voice traffic to be given priority over data. The effect on performance of various operational and design parameters such as ratio of voice to data traffic, queue limit and voice packet size is investigated. Comparisons are made where possible with related work on other protocols proposed for voice-data integration. The main conclusions are: (a) there is a general degradation of performance as the ratio of voice traffic to data traffic increases, (b) substantial improvement in performance can be achieved by restricting the queue length at data nodes and (c) for a given ring utilisation, smaller voice packets result in lower delays for both voice and data traffic.

Rotating-frame nuclear magnetic relaxation of spins diffusing on a disordered lattice: a Monte Carlo model

The rotating-frame nuclear magnetic relaxation rate of spins diffusing on a disordered lattice has been calculated by Monte Carlo methods. The disorder includes not only variation in the distances between neighbouring spin sites but also variation in the hopping rate associated with each site. The presence of the disorder, particularly the hopping rate disorder, causes changes in the time-dependent spin correlation functions which translate into asymmetry in the characteristic peak in the temperature dependence of the dipolar relaxation rate. The results may be used to deduce the average hopping rate from the relaxation but the effect is not sufficiently marked to enable the distribution of the hopping rates to be evaluated. The distribution, which is a measure of the degree of disorder, is the more interesting feature and it has been possible to show from the calculation that measurements of the relaxation rate as a function of the strength of the radiofrequency spin-locking magnetic field can lead to an evaluation of its width. Some experimental data on an amorphous metal - hydrogen alloy are reported which demonstrate the feasibility of this novel approach to rotating-frame relaxation in disordered materials.

Performance evaluation of a distributed algorithm for an inverse heat conduction problem

Numerical solutions of realistic 2-D and 3-D inverse problems may require a very large amount of computation. A two-level concept on parallelism is often used to solve such problems. The primary level uses the problem partitioning concept which is a decomposition based on the mathematical/physical problem. The secondary level utilizes the widely used data partitioning concept. A theoretical performance model is built based on the two-level parallelism. The observed performance results obtained from a network of general purpose Sun Sparc stations are compared with the theoretical values. Restrictions of the theoretical model are also discussed.

Evaluation of distortions in laser welded shipbuilding parts using local-global finite element approach

In recognition of the differences of scale between the welding pool and the heat affected zone along the welding line on one hand, and the overall size of the components being welded on the other, a local-global finite element approach was developed for the evaluation of distortions in laser welded shipbuilding parts. The approach involves the tandem use of a 'local' and a 'global' step. The local step involves a three-dimensional finite element model for the simulation of the laser welding process using the Sysweld finite element code, which takes into account thermal, metallurgical, and mechanical aspects. The simulation of the laser welding process was performed using a non-linear heat transfer analysis, based on a keyhole formation model, and a coupled transient thermomechanical analysis, which takes into account metallurgical transformations using the temperature dependent material properties and the continuous cooling transformation diagram. The size and shape of the keyhole used in the local finite element analysis was evaluated using a keyhole formation model and the Physica finite volume code. The global step involves the transfer of residual plastic strains and the stiffness of the weld obtained from the local model to the global analysis, which then provides the predicted distortions for the whole part. This newly developed methodology was applied to the evaluation of global distortions due to laser welding of stiffeners on a shipbuilding part. The approach has been proved reliable in comparison with experiments and of practical industrial use in terms of computing time and storage.

Simulating the evacuation of very large populations in large domains using a parallel implementation of the buildingEXODUS evacuation model

Computer egress simulation has potential to be used in large scale incidents to provide live advice to incident commanders. While there are many considerations which must be taken into account when applying such models to live incidents, one of the first concerns the computational speed of simulations. No matter how important the insight provided by the simulation, numerical hindsight will not prove useful to an incident commander. Thus for this type of application to be useful, it is essential that the simulation can be run many times faster than real time. Parallel processing is a method of reducing run times for very large computational simulations by distributing the workload amongst a number of CPUs. In this paper we examine the development of a parallel version of the buildingEXODUS software. The parallel strategy implemented is based on a systematic partitioning of the problem domain onto an arbitrary number of sub-domains. Each sub-domain is computed on a separate processor and runs its own copy of the EXODUS code. The software has been designed to work on typical office based networked PCs but will also function on a Windows based cluster. Two evaluation scenarios using the parallel implementation of EXODUS are described; a large open area and a 50 story high-rise building scenario. Speed-ups of up to 3.7 are achieved using up to six computers, with high-rise building evacuation simulation achieving run times of 6.4 times faster than real time.

Application of particle swarm optimisation to evaluation of polymer cure kinetics models

A particle swarm optimisation approach is used to determine the accuracy and experimental relevance of six disparate cure kinetics models. The cure processes of two commercially available thermosetting polymer materials utilised in microelectronics manufacturing applications have been studied using a differential scanning calorimetry system. Numerical models have been fitted to the experimental data using a particle swarm optimisation algorithm which enables the ultimate accuracy of each of the models to be determined. The particle swarm optimisation approach to model fitting proves to be relatively rapid and effective in determining the optimal coefficient set for the cure kinetics models. Results indicate that the singlestep autocatalytic model is able to represent the curing process more accurately than more complex model, with ultimate accuracy likely to be limited by inaccuracies in the processing of the experimental data.

Formalised peer mentoring pilot evaluation

Over the past ten years, mentoring of children and young people has become an increasingly important feature of social policy in the UK. This has been mirrored in the rapid growth in the number of mentoring schemes operating. However, it is widely acknowledged that no one single definition or model of mentoring exists; rather there are a number of different models providing support to young people in a range of settings. This research was undertaken during the autumn term of 2006 and the summer term of 2007. The methodology comprised an analysis of mentoring models in the 180 participating schools; questionnaires sent to all co-ordinators and to mentors/proteges in 40 schools; interviews with co-ordinators, pupils and support agents in 8 case study schools. Includes: •Introduction •Evaluation methodology •Analysis of school pilot application forms •Evaluation results •Conclusions •Recommendations •Bibliography •Appendices

ReaderBench: Automated evaluation of collaboration based on cohesion and dialogism

Dascalu, M., Trausan-Matu, S., McNamara, D.S., & Dessus, P. (2015). ReaderBench – Automated Evaluation of Collaboration based on Cohesion and Dialogism. International Journal of Computer-Supported Collaborative Learning, 10(4), 395–423. doi: 10.1007/s11412-015-9226-y

Generalized ocean color inversion model for retrieving marine inherent optical properties

Ocean color measured from satellites provides daily, global estimates of marine inherent optical properties (IOPs). Semi-analytical algorithms (SAAs) provide one mechanism for inverting the color of the water observed by the satellite into IOPs. While numerous SAAs exist, most are similarly constructed and few are appropriately parameterized for all water masses for all seasons. To initiate community-wide discussion of these limitations, NASA organized two workshops that deconstructed SAAs to identify similarities and uniqueness and to progress toward consensus on a unified SAA. This effort resulted in the development of the generalized IOP (GIOP) model software that allows for the construction of different SAAs at runtime by selection from an assortment of model parameterizations. As such, GIOP permits isolation and evaluation of specific modeling assumptions, construction of SAAs, development of regionally tuned SAAs, and execution of ensemble inversion modeling. Working groups associated with the workshops proposed a preliminary default configuration for GIOP (GIOP-DC), with alternative model parameterizations and features defined for subsequent evaluation. In this paper, we: (1) describe the theoretical basis of GIOP; (2) present GIOP-DC and verify its comparable performance to other popular SAAs using both in situ and synthetic data sets; and, (3) quantify the sensitivities of their output to their parameterization. We use the latter to develop a hierarchical sensitivity of SAAs to various model parameterizations, to identify components of SAAs that merit focus in future research, and to provide material for discussion on algorithm uncertainties and future emsemble applications.

An Evaluation of the Impact of the Prospective Payment System on Antidepressant Use in Nursing Home Residents

Objectives: To determine the impact of the prospective payment system (PPS) for skilled nursing facilities on the pharmacologic treatment of depression.

Methods: We used a quasi-experimental study comparing the pharmacological treatment rates for depression in the pre-PPS period (1997) to the post-PPS period (2000) in 8149 residents with documented depression living in over 500 nursing facilities in Ohio. Logistic regression models adjusting for clustering effects of residents residing in homes using generalized estimating equations provided estimates of the PPS effect on use of any antidepressant and the use of selective serotonin reuptake inhibitors (SSRIs). We evaluated the extent to which the PPS effect was modified by organizational characteristics, including structural characteristics, resource characteristics, and staff resources available in the homes.

Results: Overall, there was no difference in the likelihood of any antidepressant [odds ratio (OR), 1.05; 95% confidence interval (CI), 0.93 to 1.18, resident-adjusted model] or an SSRI being used (OR, 0.98; 95% CI, 0.86 to 1.12, resident-adjusted model) after the introduction of PPS compared with 1997 when this reimbursement system was not in place (referent group). These trends did not appear to be modified substantially by organizational characteristics.

Conclusion: Although PPS did not appear to have influenced the treatment of depression in nursing homes, systems that provide checks and balances in relation to PPS are warranted.

Evaluation of a Water-soluble Bioadhesive Patch for Photodynamic Therapy of Vulval Lesions

An innovative bioadhesive patch intended primarily as a vulval drug delivery system and, specifically, as a means to deliver photosensitisers, or their prodrugs, for photodynamic purposes is described. The patch was formulated with a copolymer of methyl vinyl ether and maleic anhydride (PMVE/MA) as a bioadhesive matrix and poly(vinyl chloride) as a drug-impervious backing layer. Adhesive strength to neonate porcine skin, as a model substrate, was evaluated using peel and tensile testing measurements. Acceptabilities of non-drug loaded patches were appraised using human volunteers and visual-analogue scoring devices. An optimal formulation, with water uptake and peel strengths appropriate for vulval drug delivery, was cast from a 20% (w/w) PMVE/MA solution and adhered with a strength of approximately 1.7 N cm-2. Patient evaluation demonstrated comfort and firm attachment for up to 4 h in mobile patients. Aminolevulinic acid, a commonly used photosensitiser, was formulated into the candidate formulation and applied to vulval intraepithelial neoplastic lesions. Fluorescence under ultraviolet illumination revealed protoporphyrin synthesis. The patch achieves the extended application times obligatory in topical photodynamic therapy of vulval lesions, thereby contributing to potential methods for the eradication of neoplastic lesions in the lower female reproductive tract.

An Experimental and Predictive Evaluation of Unsteady Gas Flow through Automotive Catalyst Elements

The incorporation of one-dimensional simulation codes within engine modelling applications has proved to be a useful tool in evaluating unsteady gas flow through elements in the exhaust system. This paper reports on an experimental and theoretical investigation into the behaviour of unsteady gas flow through catalyst substrate elements. A one-dimensional (1-D) catalyst model has been incorporated into a 1-D simulation code to predict this behaviour.

Experimental data was acquired using a ‘single pulse’ test rig. Substrate samples were tested under ambient conditions in order to investigate a range of regimes experienced by the catalyst during operation. This allowed reflection and transmission characteristics to be quantified in relation to both geometric and physical properties of substrate elements. Correlation between measured and predicted results is demonstrably good and the model provides an effective analysis tool for evaluating unsteady gas flow through different catalytic converter designs.