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Papers by Maura E Monville

MicroRNAs are a hot topic of research in molecular biology. Their role is however still to be elu... more MicroRNAs are a hot topic of research in molecular biology. Their role is however still to be elucidated in full. We present a data-oriented approach to the study of microRNA-gene interactions, building heavily on methods of document analysis. The paper aims at illustrating an approach rather than specific methods of analysis, however some sample results are also presented, which show how latent information can be exploited to suggest directions for laboratory experiments, thus avoiding unnecessary expense in time and resources.

Physica Medica, 2014

This study is part of a project concerned with real-time EPID-based verification of the increment... more This study is part of a project concerned with real-time EPID-based verification of the incremental dose delivered during IMRT radiation treatments. Three automated Monte-Carlo methods are devised to calculate the differential dose delivered to the EPID during treatment. All methods break down the normalized total monitor units into a number of equally spaced segments. A method models the dynamic simulation as a series of static fields, each field corresponding to an IMRT segment or a sub-segment. Another method models each segment as a separate dynamic IMRT file. A third method, which modifies the DYNVMLC module of the BEAMnrc code, uses the full-MLC file. The MLC positions for the simulated photons are sequentially selected within DYNVMLC to correspond to individual segments of the delivery. A bash script calls the BEAM shared-library to calculate and store the EPID dose for each segment. Validation is performed by comparing the average dose contributed by all segments with the dose predicted by a canonical dynamic IMRT simulation that uses the same MLC file. The best results are achieved by the methods based on dynamic simulations (where leaf positions within a segment are interpolated for simulated photons) whose normalized root mean square error is at the most 0.2% over the focal area. EPID images can be predicted for individual segments (or smaller intervals) of an IMRT delivery using Monte-Carlo methods. The MLC file can be externally spliced or a simple modification of the DYNVMLC code can achieve accurate results.

Journal of Physics: Conference Series, 2014

View the article online for updates and enhancements. You may also like A back-projection algorit... more View the article online for updates and enhancements. You may also like A back-projection algorithm in the presence of an extra attenuating medium: towards EPID dosimetry for the MR-Linac I Torres-Xirau, I Olaciregui-Ruiz, R A Rozendaal et al.-Clinical implementation and rapid commissioning of an EPID based in-vivo dosimetry system

Computer Physics Communications, 2008

Over the last decade it has been shown theoretically and experimentally that a near-resonant stan... more Over the last decade it has been shown theoretically and experimentally that a near-resonant standing wave light field can be used during deposition to deflect collimated neutral atoms, thereby constraining them to form periodic structures. Another effect studied in recent experiments is that a laser interference pattern in contact with a substrate can also result in patterns mimicking the interference fringes. This patterning has tentatively been attributed to thermal gradients resulting from non-uniform heating induced by the interference patterns. We developed a model and a computer program to investigate the possibility of making these two laser effects interact constructively to refine the resolution. The simulations proceed in two stages: first, atom trajectories in a laser field are simulated using classical-mechanical equations of motion in an effective potential to obtain the deposition profile; then, the obtained profile is used as an input in a kinetic Monte Carlo (KMC) simulation of atom diffusion on a substrate with spatially varying temperature. Our results show substantial improvement in quality of the patterns compared to that achieved by using either effect alone. We examine many growth conditions in addition to the different laser parameter settings for optimal constructive interference of the two effects. The computer code used in the simulations is designed to run efficiently on both simple PC platforms and supercomputers; its design, data structures used and other features are described in detail.

Annals of Nuclear Energy, 2012

We present an empirical model that describes the yield of gamma rays emitted by fission in the ti... more We present an empirical model that describes the yield of gamma rays emitted by fission in the time interval from 20 to 958 ns following a fission event. The analysis is based on experimental data from neutron-induced fission of 235 U and 239 Pu. The model is devised by first using regression analysis to identify likely patterns in the data and to choose plausible fitting functions. We provide statistical and physical arguments in support of time and energy independence. The intensity of the emitted gamma rays can be described as a bivariate distribution that is the product of independent variates for energy and time. We test several plausible distribution families for the energy and time variates and use maximum likelihood and minimum v 2 to estimate distribution parameters. Because of the uncertainty in the experimental data, multiple combinations of variate pairs give rise to a surface that plausibly well fits the observations well. The best-fit variate turns out to be lognormal in energy and F in time. The findings illustrated in this paper can be used to simulate gamma ray de-excitation from fission in Monte Carlo codes.

It is known that atoms being deposited onto a substrate can be manipulated using laser beams befo... more It is known that atoms being deposited onto a substrate can be manipulated using laser beams before deposition and form periodic structures [1]. This effect is due to interaction of induced dipole moments of atoms with the standing wave of the laser beams. More recently, periodic pattern formation after deposition caused by anisotropic diffusion due to non-uniform heating of the

Nuclear Science and Engineering, 2007

We describe the implementation of algorithms related to the delayed neutron production in photon-... more We describe the implementation of algorithms related to the delayed neutron production in photon-induced fission on actinides. The algorithms are based on data from experiments and have been implemented in the MCNP-PoliMi code. The modified code is being used to design and analyze methods to identify concealed highly enriched uranium with a system based on the use of photon interrogation

2007 IEEE Particle Accelerator Conference (PAC), 2007

At the LHC upgrade luminosity of 10 35 cm-2 s-1 , collision product power in excess of a kW is de... more At the LHC upgrade luminosity of 10 35 cm-2 s-1 , collision product power in excess of a kW is deposited in the inner triplet quadrupoles. The quadrupole field sweeps secondary particles from pp-collisions into the superconducting (SC) coils, concentrating the power deposition at the magnetic mid-planes. The local peak power density can substantially exceed the conductor quench limits and reduce component lifetime. Under these conditions, block-coil geometries may result in overall improved performance by removing the superconductor from the magnetic mid-planes and/or allowing increased shielding at such locations. First realistic energy deposition simulations are performed for an interaction region based on block-coil quadrupoles with parameters suitable for the LHC upgrade. Results are presented on distributions of power density and accumulated dose in the inner triplet components as well as on dynamic heat loads on the cryogenic system. Optimization studies are performed on configuration and parameters of the beam pipe, cold bore and cooling channels. The feasibility of the proposed design is discussed.

The truncated Cornish-Fisher inverse expansion is well known. It is used, for example, to approxi... more The truncated Cornish-Fisher inverse expansion is well known. It is used, for example, to approximate value-at-risk and conditional value-at-risk. It is known that this expansion gives a distribution for limited skewness and kurtosis and that the distribution may be a poor fit. drawing on Maillard (2012) we show how to find a unique corrected Cornish-Fisher distribution efficiently for a wide range of skewness and kurtosis. We show it has a unimodal density and a quantile function that is twice continuously differentiable as a function of mean, variance, skewness and kurtosis. We show how to obtain random variates efficiently and how to test goodness-of-fit. We apply the Cornish-Fisher distribution to fit hedge-fund returns and estimate conditional value-at risk. Finally, we investigate various generalisations of the Cornish-Fisher distributions and show they do not have the same desirable properties.

MicroRNAs are a hot topic of research in molecular biology. Their role is however still to be elu... more MicroRNAs are a hot topic of research in molecular biology. Their role is however still to be elucidated in full. We present a data-oriented approach to the study of microRNA-gene interactions, building heavily on methods of document analysis. The paper aims at illustrating an approach rather than specific methods of analysis, however some sample results are also presented, which show how latent information can be exploited to suggest directions for laboratory experiments, thus avoiding unnecessary expense in time and resources.

Physica Medica, 2014

This study is part of a project concerned with real-time EPID-based verification of the increment... more This study is part of a project concerned with real-time EPID-based verification of the incremental dose delivered during IMRT radiation treatments. Three automated Monte-Carlo methods are devised to calculate the differential dose delivered to the EPID during treatment. All methods break down the normalized total monitor units into a number of equally spaced segments. A method models the dynamic simulation as a series of static fields, each field corresponding to an IMRT segment or a sub-segment. Another method models each segment as a separate dynamic IMRT file. A third method, which modifies the DYNVMLC module of the BEAMnrc code, uses the full-MLC file. The MLC positions for the simulated photons are sequentially selected within DYNVMLC to correspond to individual segments of the delivery. A bash script calls the BEAM shared-library to calculate and store the EPID dose for each segment. Validation is performed by comparing the average dose contributed by all segments with the dose predicted by a canonical dynamic IMRT simulation that uses the same MLC file. The best results are achieved by the methods based on dynamic simulations (where leaf positions within a segment are interpolated for simulated photons) whose normalized root mean square error is at the most 0.2% over the focal area. EPID images can be predicted for individual segments (or smaller intervals) of an IMRT delivery using Monte-Carlo methods. The MLC file can be externally spliced or a simple modification of the DYNVMLC code can achieve accurate results.

Journal of Physics: Conference Series, 2014

View the article online for updates and enhancements. You may also like A back-projection algorit... more View the article online for updates and enhancements. You may also like A back-projection algorithm in the presence of an extra attenuating medium: towards EPID dosimetry for the MR-Linac I Torres-Xirau, I Olaciregui-Ruiz, R A Rozendaal et al.-Clinical implementation and rapid commissioning of an EPID based in-vivo dosimetry system

Computer Physics Communications, 2008

Over the last decade it has been shown theoretically and experimentally that a near-resonant stan... more Over the last decade it has been shown theoretically and experimentally that a near-resonant standing wave light field can be used during deposition to deflect collimated neutral atoms, thereby constraining them to form periodic structures. Another effect studied in recent experiments is that a laser interference pattern in contact with a substrate can also result in patterns mimicking the interference fringes. This patterning has tentatively been attributed to thermal gradients resulting from non-uniform heating induced by the interference patterns. We developed a model and a computer program to investigate the possibility of making these two laser effects interact constructively to refine the resolution. The simulations proceed in two stages: first, atom trajectories in a laser field are simulated using classical-mechanical equations of motion in an effective potential to obtain the deposition profile; then, the obtained profile is used as an input in a kinetic Monte Carlo (KMC) simulation of atom diffusion on a substrate with spatially varying temperature. Our results show substantial improvement in quality of the patterns compared to that achieved by using either effect alone. We examine many growth conditions in addition to the different laser parameter settings for optimal constructive interference of the two effects. The computer code used in the simulations is designed to run efficiently on both simple PC platforms and supercomputers; its design, data structures used and other features are described in detail.

Annals of Nuclear Energy, 2012

We present an empirical model that describes the yield of gamma rays emitted by fission in the ti... more We present an empirical model that describes the yield of gamma rays emitted by fission in the time interval from 20 to 958 ns following a fission event. The analysis is based on experimental data from neutron-induced fission of 235 U and 239 Pu. The model is devised by first using regression analysis to identify likely patterns in the data and to choose plausible fitting functions. We provide statistical and physical arguments in support of time and energy independence. The intensity of the emitted gamma rays can be described as a bivariate distribution that is the product of independent variates for energy and time. We test several plausible distribution families for the energy and time variates and use maximum likelihood and minimum v 2 to estimate distribution parameters. Because of the uncertainty in the experimental data, multiple combinations of variate pairs give rise to a surface that plausibly well fits the observations well. The best-fit variate turns out to be lognormal in energy and F in time. The findings illustrated in this paper can be used to simulate gamma ray de-excitation from fission in Monte Carlo codes.

It is known that atoms being deposited onto a substrate can be manipulated using laser beams befo... more It is known that atoms being deposited onto a substrate can be manipulated using laser beams before deposition and form periodic structures [1]. This effect is due to interaction of induced dipole moments of atoms with the standing wave of the laser beams. More recently, periodic pattern formation after deposition caused by anisotropic diffusion due to non-uniform heating of the

Nuclear Science and Engineering, 2007

We describe the implementation of algorithms related to the delayed neutron production in photon-... more We describe the implementation of algorithms related to the delayed neutron production in photon-induced fission on actinides. The algorithms are based on data from experiments and have been implemented in the MCNP-PoliMi code. The modified code is being used to design and analyze methods to identify concealed highly enriched uranium with a system based on the use of photon interrogation

2007 IEEE Particle Accelerator Conference (PAC), 2007

At the LHC upgrade luminosity of 10 35 cm-2 s-1 , collision product power in excess of a kW is de... more At the LHC upgrade luminosity of 10 35 cm-2 s-1 , collision product power in excess of a kW is deposited in the inner triplet quadrupoles. The quadrupole field sweeps secondary particles from pp-collisions into the superconducting (SC) coils, concentrating the power deposition at the magnetic mid-planes. The local peak power density can substantially exceed the conductor quench limits and reduce component lifetime. Under these conditions, block-coil geometries may result in overall improved performance by removing the superconductor from the magnetic mid-planes and/or allowing increased shielding at such locations. First realistic energy deposition simulations are performed for an interaction region based on block-coil quadrupoles with parameters suitable for the LHC upgrade. Results are presented on distributions of power density and accumulated dose in the inner triplet components as well as on dynamic heat loads on the cryogenic system. Optimization studies are performed on configuration and parameters of the beam pipe, cold bore and cooling channels. The feasibility of the proposed design is discussed.

The truncated Cornish-Fisher inverse expansion is well known. It is used, for example, to approxi... more The truncated Cornish-Fisher inverse expansion is well known. It is used, for example, to approximate value-at-risk and conditional value-at-risk. It is known that this expansion gives a distribution for limited skewness and kurtosis and that the distribution may be a poor fit. drawing on Maillard (2012) we show how to find a unique corrected Cornish-Fisher distribution efficiently for a wide range of skewness and kurtosis. We show it has a unimodal density and a quantile function that is twice continuously differentiable as a function of mean, variance, skewness and kurtosis. We show how to obtain random variates efficiently and how to test goodness-of-fit. We apply the Cornish-Fisher distribution to fit hedge-fund returns and estimate conditional value-at risk. Finally, we investigate various generalisations of the Cornish-Fisher distributions and show they do not have the same desirable properties.