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  • MR-Guided Adaptive Radiotherapy for OAR Sparing in Head and Neck Cancers 

    Mulder, Samuel L.; Heukelom, Jolien; McDonald, Brigid A.; Van Dijk, Lisanne; Wahid, Kareem A.; (2022)
    MR-linac devices offer the potential for advancements in radiotherapy (RT) treatment of head and neck cancer (HNC) by using daily MR imaging performed at the time and setup of treatment delivery. This article aims to present a review of current adaptive RT (ART) methods on MR-Linac devices directed towards the sparing of organs at risk (OAR) and a ...
  • Chromosome size affects sequence divergence between species through the interplay of recombination and selection 

    Tigano, Anna; Khan, Ruqayya; Omer, Arina D.; Weisz, David; Dudchenko, Olga; (2022)
    The structure of the genome shapes the distribution of genetic diversity and sequence divergence. To investigate how the relationship between chromosome size and recombination rate affects sequence divergence between species, we combined empirical analyses and evolutionary simulations. We estimated pairwise sequence divergence among 15 species from ...
  • Severity of radiation pneumonitis, from clinical, dosimetric and biological features: a pilot study 

    Aso, Samantha; Navarro‑Martin, Arturo; Castillo, Richard; Padrones, Susana; Castillo, Edward; (2020)
    Background and objective: Radiation pneumonitis (RP) could be a lethal complication of lung cancer treatment. No reliable predictors of RP severity have been recognized. This prospective pilot study was performed to identify early predictors of high grade lung toxicity and to evaluate clinical, biological or dosimetric features associated with different ...
  • Extubation Failure in Critically Ill COVID-19 Patients: Risk Factors and Impact on In-Hospital Mortality 

    Ionescu, Filip; Zimmer, Markie S.; Petrescu, Ioana; Castillo, Edward; Bozyk, Paul; (2021)
    Purpose:We sought to identify clinical factors that predict extubation failure (reintubation) and its prognostic implications in critically ill COVID-19 patients.Materials and Methods:Retrospective, multi-center cohort study of hospitalized COVID-19 patients. Multivariate competing risk models were employed to explore the rate of reintubation and its ...
  • Functional avoidance-based intensity modulated proton therapy with 4DCT derived ventilation imaging for lung cancer 

    Dougherty, Jingjing M.; Castillo, Edward; Castillo, Richard; Faught, Austin M.; Pepin, Mark; (2021)
    The primary objective is to evaluate the potential dosimetric gains of performing functional avoidance-based proton treatment planning using 4DCT derived ventilation imaging. 4DCT data of 31 patients from a prospective functional avoidance clinical trial were evaluated with intensity modulated proton therapy (IMPT) plans and compared with clinical ...
  • Chromatin architecture transitions from zebrafish sperm through early embryogenesis 

    Wike, Candice L.; Guo, Yixuan; Tan, Mengyao; Nakamura, Ryohei; Shaw, Dana Klatt; (2021)
    Chromatin architecture mapping in 3D formats has increased our understanding of how regulatory sequences and gene expression are connected and regulated in a genome. The 3D chromatin genome shows extensive remodeling during embryonic development, and although the cleavage-stage embryos of most species lack structure before zygotic genome activation ...
  • Quantifying pulmonary perfusion from noncontrast computed tomography 

    Castillo, Edward; Nair, Girish; Turner‐Lawrence, Danielle; Myziuk, Nicholas; Emerson, Scott; (2021)
    Purpose: Computed tomography (CT)-derived ventilation methods compute respiratory induced volume changes as a surrogate for pulmonary ventilation. Currently, there are no known methods to derive perfusion information from noncontrast CT. We introduce a novel CT-Perfusion (CT-P) method for computing the magnitude mass changes apparent on dynamic ...
  • Reciprocity-gap misfit functional for distributed acoustic sensing, combining data from passive and active sources 

    Faucher, Florian; de Hoop, Maarten V.; Scherzer, Otmar (2021)
    Quantitative imaging of subsurface earth properties in elastic media is performed from distributed acoustic sensing data. A new misfit functional based upon the reciprocity gap is designed, taking crosscorrelations of displacement and strain, and these products further associate an observation with a simulation. In comparison with other misfit ...
  • Clustering earthquake signals and background noises in continuous seismic data with unsupervised deep learning 

    Seydoux, Léonard; Balestriero, Randall; Poli, Piero; de Hoop, Maarten; Campillo, Michel; (2020)
    The continuously growing amount of seismic data collected worldwide is outpacing our abilities for analysis, since to date, such datasets have been analyzed in a human-expert-intensive, supervised fashion. Moreover, analyses that are conducted can be strongly biased by the standard models employed by seismologists. In response to both of these ...
  • Convergence of a Class of Stationary Iterative Methods for Saddle Point Problems 

    Zhang, Yin (2019)
    A unified convergence theory is derived for a class of stationary iterative methods for solving linear equality constrained quadratic programs or saddle point problems. This class is constructed from essentially all possible splittings of the submatrix residing in the (1,1)-block of the augmented saddle point matrix that would produce non-expansive ...
  • An accelerated Poisson solver based on multidomain spectral discretization 

    Babb, Tracy; Gillman, Adrianna; Hao, Sijia; Martinsson, Per-Gunnar (2018)
    This paper presents a numerical method for variable coefficient elliptic PDEs with mostly smooth solutions on two dimensional domains. The method works best for domains that can readily be mapped onto a rectangle, or a collection of nonoverlapping rectangles. The PDE is discretized via a multi-domain spectral collocation method of high local order ...
  • Weight‐adjusted discontinuous Galerkin methods: Matrix‐valued weights and elastic wave propagation in heterogeneous media 

    Chan, Jesse (2018)
    Weight‐adjusted inner products are easily invertible approximations to weighted L2 inner products. These approximations can be paired with a discontinuous Galerkin (DG) discretization to produce a time‐domain method for wave propagation which is low storage, energy stable, and high‐order accurate for arbitrary heterogeneous media and curvilinear ...
  • On discretely entropy conservative and entropy stable discontinuous Galerkin methods 

    Chan, Jesse (2018)
    High order methods based on diagonal-norm summation by parts operators can be shown to satisfy a discrete conservation or dissipation of entropy for nonlinear systems of hyperbolic PDEsᅠ[1],ᅠ[2]. These methods can also be interpreted as nodal discontinuous Galerkin methods with diagonal mass matricesᅠ[3],ᅠ[4],ᅠ[5],ᅠ[6]. In this work, we describe how ...
  • Multi-patch discontinuous Galerkin isogeometric analysis for wave propagation: Explicit time-stepping and efficient mass matrix inversion 

    Chan, Jesse; Evans, John A. (2018)
    We present a class of spline finite element methods for time-domain wave propagation which are particularly amenable to explicit time-stepping. The proposed methods utilize a discontinuous Galerkin discretization to enforce continuity of the solution field across geometric patches in a multi-patch setting, which yields a mass matrix with convenient ...
  • Topological Schemas of Memory Spaces 

    Babichev, Andrey; Dabaghian, Yuri A. (2018)
    Hippocampal cognitive map-a neuronal representation of the spatial environment-is widely discussed in the computational neuroscience literature for decades. However, more recent studies point out that hippocampus plays a major role in producing yet another cognitive framework-the memory space-that incorporates not only spatial, but also non-spatial ...
  • Discretization of Multipole Sources in a Finite Difference Setting for Wave Propagation Problems 

    Bencomo, Mario J.; Symes, William (2018-06-20)
    Seismic sources are commonly idealized as point-sources due to their small spatial extent relative to seismic wavelengths. The acoustic isotropic point-radiator is inadequate as a model of seismic wave generation for seismic sources that are known to exhibit directivity. Therefore, accurate modeling of seismic wavefields must include source representations ...
  • Compositional heterogeneity near the base of the mantle transition zone beneath Hawaii 

    Yu, Chunquan; Day, Elizabeth A.; de Hoop, Maarten V.; Campillo, Michel; Goes, Saskia; (2018)
    Global seismic discontinuities near 410 and 660 km depth in Earth’s mantle are expressions of solid-state phase transitions. These transitions modulate thermal and material fluxes across the mantle and variations in their depth are often attributed to temperature anomalies. Here we use novel seismic array analysis of SSwaves reflecting off ...
  • Reduced order modeling for time-dependent optimization problems with initial value controls 

    Heinkenschloss, Matthias; Jando, Dörte (2018)
    This paper presents a new reduced order model (ROM) Hessian approximation for linear-quadratic optimal control problems where the optimal control is the initial value. Such problems arise in parameter identification and data assimilation, where the parameters to be identified appear in the initial data, and also as subproblems in multiple shooting ...
  • An exact redatuming procedure for the inverse boundary value problem for the wave equation 

    de Hoop, Maarten V.; Kepley, Paul; Oksanen, Lauri (2018)
    Redatuming is a data processing technique to transform measurements recorded in one acquisition geometry to an analogous data set corresponding to another acquisition geometry, for which there are no recorded measurements. We consider a redatuming problem for a wave equation on a bounded domain, or on a manifold with boundary, and model data acquisition ...
  • Mapping Mantle Transition Zone Discontinuities Beneath the Central Pacific With Array Processing ofᅠSSᅠPrecursors 

    Yu, Chunquan; Day, Elizabeth A.; de Hoop, Maarten V.; Campillo, Michel; van der Hilst, Robert D. (2017)
    We image mantle transition zone (MTZ) discontinuities beneath the Central Pacific using ~120,000 broadband SS waveforms. With a wave packet‐based array processing technique (curvelet transform), we improve the signal‐to‐noise ratio of SS precursors and remove interfering phases, so that precursors can be identified and measured over a larger distance ...

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