bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spectral characterization of tissues in high spectral and spatial resolution MR images: Implications for a classification‐based synthetic CT algorithm
Authors: Wood Abbie M. , Shea Steven M. , Medved Milica , Karczmar Gregory S. , Surucu Murat , Gros Sebastien , Small William , Roeske John 
Published: February 2017

PurposeTo characterize the spectral parameters of tissues with high spectral and spatial resolution magnetic resonance images to be used as a foundation for a classification‐based synthetic CT algorithm.MethodsA phantom was constructed consisting of a section of fresh beef leg with bone embedded in 1% agarose gel. The high spectral and spatial (HiSS) resolution MR imaging sequence used had 1.0 mm in‐plane resolution and 11.1 Hz spectral resolution. This sequence was used to image the phantom and one patient. Post‐processing was performed off‐line with IDL and included Fourier transformation of the time‐domain data, labeling of fat and water peaks, and fitting the magnitude spectra with Lorentzian functions. Images of the peak height and peak integral of both the water and fat resonances were generated and analyzed. Several regions‐of‐interest (ROIs) were identified in phantom: bone marrow, cortical bone, adipose tissue, muscle, agar gel, and air; in the patient, no agar gel was present but an ROI of saline in the bladder was analyzed. All spectra were normalized by the noise within each voxel; thus, all parameters are reported in terms of signal‐to‐noise (SNR). The distributions of tissue spectral parameters were analyzed and scatterplots generated. Water peak height in cortical bone was compared to air using a nonparametric t‐test. Composition of the various ROIs in terms of water, fat, or fat and water was also reported.ResultsIn phantom, the scatterplot of peak height (water versus fat) showed good separation of bone marrow and adipose tissue. Water versus fat integral scatterplot showed better separation of muscle and cortical bone than the peak height scatterplot. In the patient data, the distributions of water and fat peak heights were similar to that in phantom, with more overlap of bone marrow and cortical bone than observed in phantom. The relationship between bone marrow and cortical bone for peak integral was better separated than those of peak heights in the patient data. For both the phantom and patient, there was a significant amount of overlap in spectral parameters of cortical bone versus air.ConclusionThese results show promising results for utilizing HiSS imaging in a classification‐based synthetic CT algorithm. Cortical bone and air overlap was expected due to the short T2* of bone; reducing early echo times would improve the SNR in bone and image data from these early echoes could help differentiate these tissue types. Further studies need to be done with the goal of better separation of air and bone, and to extend the concept to volumetric imaging before it can be clinically applied.
An effective noise reduction method for multi‐energy CT images that exploit spatio‐spectral features
Authors: Li Zhoubo , Leng Shuai , Yu Lifeng , Manduca Armando , McCollough Cynthia H. 
Published: February 2017

PurposeTo develop and evaluate an image‐domain noise reduction method for multi‐energy CT (MECT) data.MethodsMulti‐Energy Non‐Local Means (MENLM) is a technique that uses the redundant information in MECT images to achieve noise reduction. In this method, spatio‐spectral features are used to determine the similarity between pixels, making the similarity evaluation more robust to image noise. The performance of this MENLM filter was tested on images acquired on a whole‐body research photon counting CT system. The impact of filtering on image quality was quantitatively evaluated in phantom studies in terms of image noise level (standard deviation of pixel values), noise power spectrum (NPS), in‐plane and cross‐plane spatial resolution, CT number accuracy, material decomposition performance, and subjective low‐contrast spatial resolution using the American College of Radiology (ACR) CT accreditation phantom. Clinical feasibility was assessed by performing MENLM on contrast‐enhanced swine images and unenhanced cadaver head images using clinically relevant doses and dose rates.ResultsThe phantom studies demonstrated that the MENLM filter reduced noise substantially and still preserved the shape and peak frequency of the NPS. With 80% noise reduction, MENLM filtering caused no degradation of high‐contrast spatial resolution, as illustrated by the modulation transfer function (MTF) and slice sensitivity profile (SSP). CT number accuracy was also maintained for all energy channels, demonstrating that energy resolution was not affected by filtering. Material decomposition performance was improved with MENLM filtering. The subjective evaluation using the ACR phantom demonstrated an improvement in low‐contrast performance. MENLM achieved effective noise reduction in both contrast‐enhanced swine images and unenhanced cadaver head images, resulting in improved detection of subtle vascular structures and the differentiation of white/gray matter.ConclusionIn MECT, MENLM achieved around 80% noise reduction and greatly improved material decomposition performance and the detection of subtle anatomical/low‐contrast features while maintaining spatial and energy resolution. MENLM filtering may improve diagnostic or functional analysis accuracy and facilitate radiation dose and contrast media reduction for MECT.
Targeted dose enhancement in radiotherapy for breast cancer using gold nanoparticles, part 2: A treatment planning study
Authors: Strigari Lidia , Ferrero Veronica , Visonà Giovanni , Dalmasso Federico , Gobbato Andrea , Cerello Piergiorgio , Visentin Sonja , Attili Andrea 
Published: February 2017

PurposeIn recent years, there has been growing interest in the use of gold nanoparticles (GNPs) combined with radiotherapy to improve tumor control. However, the complex interplay between GNP uptake and dose distribution in realistic clinical treatment are still somewhat unknown.MethodsThe effects of different concentrations of 2 nm diameter GNP, ranging from 0 to nanoparticles per tumoral cell, were theoretically investigated. A parametrization of the GNP distribution outside the target was carried out using a Gaussian standard deviation σ, from a zero value, relative to a selective concentration of GNPs inside the tumor volume alone, to 50mm, when GNPs are spatially distributed also in the healthy tissues surrounding the tumor. Treatment simulations of five patients with breast cancer were performed with 6 and 15 MV photons assuming a partial breast irradiation. A closed analytical reformulation of the Local Effect Model coupled with the estimation of local dose deposited around a GNP was validated using an in vitro study for MDA‐MB‐231 tumoral cells. The expected treatment outcome was quantified in terms of tumor control probability (TCP) and normal tissue complication probability (NTCP) as a function of the spatially varying gold uptake.ResultsBreast cancer treatment planning simulations show improved treatment outcomes when GNPs are selectively concentrated in the tumor volume (i.e., σ = 0 mm). In particular, the TCP increases up to 18% for nanoparticles per cell in the tumor region depending on the treatment schedules, whereas an improvement of the therapeutic index is observed only for concentrations of about GNPs per tumoral cell and limited spatial distribution in the normal tissue.ConclusionsThe model provides a useful framework to estimate the nanoparticle‐driven radiosensitivity in breast cancer treatment irradiation, accounting for the complex interplay between dose and GNP uptake distributions.
On the relative performance of edge illumination x‐ray phase‐contrast CT and conventional, attenuation‐based CT
Authors: Hagen Charlotte Klara , Diemoz Paul Claude , Olivo Alessandro 
Published: February 2017

PurposeThis article is aimed at comparing edge illumination (EI) x‐ray phase contrast computed tomography (PCT) and conventional (attenuation‐based) computed tomography (CT), based on their respective contrast and noise transfer.MethodsThe noise in raw projections obtained with EI PCT is propagated through every step of the data processing, including phase retrieval and tomographic reconstruction, leading to a description of the noise in the reconstructed phase tomograms. This is compared to the noise in corresponding attenuation tomograms obtained with CT. Specifically, a formula is derived that allows evaluating the relative performance of both modalities on the basis of their contrast‐to‐noise ratio (CNR), for a variety of experimental parameters.ResultsThe noise power spectra of phase tomograms are shifted towards lower spatial frequencies, leading to a fundamentally different noise texture. The relative performance of EI PCT and CT, in terms of their CNR, is linked to spatial resolution: the CNR in phase tomograms is generally superior to that in attenuation tomograms for higher spatial resolutions (tens to hundreds of μm), but inferior for lower spatial resolutions (hundreds of μm to mm).ConclusionThese results imply that EI PCT could outperform CT in applications for which high spatial resolutions are key, e.g., small animal or specimen imaging.
Targeted dose enhancement in radiotherapy for breast cancer using gold nanoparticles, part 1: A radiobiological model study
Authors: Ferrero Veronica , Visonà Giovanni , Dalmasso Federico , Gobbato Andrea , Cerello Piergiorgio , Strigari Lidia , Visentin Sonja , Attili Andrea 
Published: February 2017

PurposeGold nanoparticles (GNPs) are being proposed in combination with radiotherapy to improve tumor control. However, the exact mechanisms underlying GNP radiosensitization are yet to be understood, thus, we present a new approach to estimate the nanoparticle‐driven increase in radiosensitivity.MethodsA stochastic radiobiological model, derived from the Local Effect Model (LEM), was coupled with Monte Carlo simulations to estimate the increase in radiosensitivity produced by the interactions between photons and GNPs at nanometric scale. The model was validated using in vitro survival data of MDA‐MB‐231 breast cancer cells containing different concentrations of 2 nm diameter GNPs receiving different doses using 160 kVp, 6 MV, and 15 MV photons. A closed analytical formulation of the model was also derived and a study of RBE and TCP behavior was conducted.ResultsResults support the increased radiosensitivity due to GNP‐driven dose inhomogeneities on a nanometric scale. The model is in good agreement with experimental clonogenic survival assays for 160 kVp, 6 MV, and 15 MV photons. The model suggests a RBE and TCP enhancement when lower energies and lower doses per fraction are used in the presence of GNPs.ConclusionsThe evolution of the local effect model was implemented to assess cellular radiosensitization in the presence of GNPs and then validated with in vitro data. The model provides a useful framework to estimate the nanoparticle‐driven radiosensitivity in treatment irradiations and could be applied to real clinical treatment predictions (described in a second part of this paper)
A decomposition technique of generalized degrees of freedom for mixedmode crack problems
Authors: Fan Huo , Zheng Hong , Li Chunguang , He Siming 
Published: February 2017

SummaryThe numerical manifold method (NMM) builds up a unified framework that is used to describe continuous and discontinuous problems; it is an attractive method for simulating a cracking phenomenon. Taking into account the differences between the generalized degrees of freedom of the physical patch and nodal displacement of the element in the NMM, a decomposition technique of generalized degrees of freedom is deduced for mixed mode crack problems. An analytic expression of the energy release rate, which is caused by a virtual crack extension technique, is proposed. The necessity of using a symmetric mesh is demonstrated in detail by analysing an additional error that had previously been overlooked. Because of this necessity, the local mathematical cover refinement is further applied. Finally, four comparison tests are given to illustrate the validity and practicality of the proposed method. The aforementioned aspects are all implemented in the high‐order NMM, so this study can be regarded as the development of the virtual crack extension technique and can also be seen as a prelude to an h‐version high‐order NMM. Copyright © 2017 John Wiley & Sons, Ltd.
A scaled boundary radial point interpolation method for 2‐D elasticity problems
Authors: Hajiazizi Mohammad , Graili Adel 
Published: February 2017

SummaryThe scaled boundary radial point interpolation method (SBRPIM), a new semi‐analytical technique, is introduced and applied to the analysis of the stress–strain problems. The proposed method combines the advantages of the scaled boundary finite element method and the boundary radial point interpolation method. In this method, no mesh is required, nodes are scattered only on the boundary of the domain, no fundamental solution is required, and as the shape functions constructed based on the radial point interpolation method possess the Kronecker delta function property, the boundary conditions of problems can be imposed accurately without additional efforts. The main ideas of the SBRPIM are introducing a new method based on boundary scattered nodes without the need to element connectivity information, satisfying Kronecker delta function property, and being capable to handle singular problems. The equations of the SBRPIM in stress–strain fields are outlined in this paper. Several benchmark examples of 2‐D elastostatic are analyzed to validate the accuracy and efficiency of the proposed method. It is found that the SBRPIM is very easy to implement and the obtained results of the proposed method show a very good agreement with the analytical solution. Copyright © 2017 John Wiley & Sons, Ltd.
A multilevel projection‐based model order reduction framework for nonlinear dynamic multiscale problems in structural and solid mechanics
Authors: Zahr Matthew J. , Avery Philip , Farhat Charbel 
Published: February 2017

SummaryA reduction/hyper reduction framework is presented for dramatically accelerating the solution of nonlinear dynamic multiscale problems in structural and solid mechanics. At each scale, the dimensionality of the governing equations is reduced using the method of snapshots for proper orthogonal decomposition, and computational efficiency is achieved for the evaluation of the nonlinear reduced‐order terms using a carefully designed configuration of the energy conserving sampling and weighting method. Periodic boundary conditions at the microscales are treated as linear multipoint constraints and reduced via projection onto the span of a basis formed from the singular value decomposition of Lagrange multiplier snapshots. Most importantly, information is efficiently transmitted between the scales without incurring high‐dimensional operations. In this proposed proper orthogonal decomposition–energy conserving sampling and weighting nonlinear model reduction framework, training is performed in two steps. First, a microscale hyper reduced‐order model is constructed in situ, or using a mesh coarsening strategy, in order to achieve significant speedups even in non‐parametric settings. Next, a classical offline–online training approach is performed to build a parametric hyper reduced‐order macroscale model, which completes the construction of a fully hyper reduced‐order parametric multiscale model capable of fast and accurate multiscale simulations. A notable feature of this computational framework is the minimization, at the macroscale level, of the cost of the offline training using the in situ or coarsely trained hyper reduced‐order microscale model to accelerate snapshot acquisition. The effectiveness of the proposed hyper reduction framework at accelerating the solution of nonlinear dynamic multiscale problems is demonstrated for two problems in structural and solid mechanics. Speedup factors as high as five orders of magnitude are shown to be achievable. Copyright © 2017 John Wiley & Sons, Ltd.
A hierarchical sequential ALE poromechanics model for tire‐soil‐water interaction on fluid‐infiltrated roads
Authors: Wollny Ines , Sun WaiChing , Kaliske Michael 
Published: February 2017

SummaryThis paper introduces a hierarchical sequential arbitrary Lagrangian‐Eulerian (ALE) model for predicting the tire‐soil‐water interaction at finite deformations. Using the ALE framework, the interaction between a rolling pneumatic tire and the fluid‐infiltrated soil underneath will be captured numerically. The road is assumed to be a fully saturated two‐phase porous medium. The constitutive response of the tire and the solid skeleton of the porous medium is idealized as hyperelastic. Meanwhile, the interaction between tire, soil, and water will be simulated via a hierarchical operator‐split algorithm. A salient feature of the proposed framework is the steady state rolling framework. While the finite element mesh of the soil is fixed to a reference frame and moves with the tire, the solid and fluid constituents of the soil are flowing through the mesh in the ALE model according to the rolling speed of the tire. This treatment leads to an elegant and computationally efficient formulation to investigate the tire‐soil‐water interaction both close to the contact and in the far field. The presented ALE model for tire‐soil‐water interaction provides the essential basis for future applications, for example, to a path‐dependent frictional‐cohesive response of the consolidating soil and unsaturated soil, respectively. Copyright © 2017 John Wiley & Sons, Ltd.
Finite volume methods for elasticity with weak symmetry
Authors: Keilegavlen Eirik , Nordbotten Jan Martin 
Published: February 2017

AbstractWe introduce a new cell‐centered finite volume discretization for elasticity with weakly enforced symmetry of the stress tensor. The method is motivated by the need for robust discretization methods for deformation and flow in porous media and falls in the category of multi‐point stress approximations (MPSAs). By enforcing symmetry weakly, the resulting method has flexibility beyond previous MPSA methods. This allows for a construction of a method that is applicable to simplexes, quadrilaterals, and most planar‐faced polyhedral grids in both 2D and 3D, and in particular, the method amends a convergence failure in previous MPSA methods for certain simplex grids. We prove convergence of the new method for a wide range of problems, with conditions that can be verified at the time of discretization. We present the first set of comprehensive numerical tests for the MPSA methods in three dimensions, covering Cartesian and simplex grids, with both heterogeneous and nearly incompressible media. The tests show that the new method consistently is second order convergent in displacement, despite being the lowest order, with a rate that mostly is between 1 and 2 for stresses. The results further show that the new method is more robust and computationally cheaper than previous MPSA methods. Copyright © 2017 The Authors. International Journal for Numerical Methods in Engineering Published by John Wiley & Sons Ltd.
Regulators of mitochondrial quality control differ in subcutaneous fat of metabolically healthy and unhealthy obese monkeys
Authors: Kavanagh Kylie , Davis Ashley T. , Peters Diane E. , LeGrand Andre C. , Bharadwaj Manish S. , Molina Anthony J.A. 
Published: February 2017

ObjectiveObesity exists with and without accompanying cardiometabolic disease, termed metabolically unhealthy obesity (MUO) and healthy obesity (MHO), respectively. Underlying differences in the ability of subcutaneous (SQ) fat to respond to nutrient excess are emerging as a key pathway. This study aimed to document the first spontaneous animal model of MHO and MUO and differences in SQ adipose tissue.MethodsVervet monkeys (Chlorocebus aethiops; N = 171) were screened for metabolic syndrome. A subset of MHO and MUO monkeys (n = 6/group) had SQ fat biopsies collected for histological evaluations and examination of key mitochondrial proteins.ResultsObesity was seen in 20% of monkeys, and within this population, 31% were healthy, which mirrors human prevalence estimates. MUO monkeys had more than 60% lower adiponectin concentrations despite similar fat cell size, uncoupling protein 3, and activated macrophage abundance. However, alternatively activated/anti‐inflammatory macrophages were 70% lower. Deficiencies of 50% or more in mitochondrial quality control regulators and selected mitochondrial fission and fusion markers were observed in the SQ fat of MUO monkeys despite comparable mitochondrial content.ConclusionsA novel and translatable spontaneously obese animal model of MHO and MUO, occurring independently of dietary factors, was characterized. Differences in mitochondrial quality and inflammatory cell populations of subcutaneous fat may underpin divergent metabolic health.
Comparison of density functionals for the study of the high spin low spin gap in Fe(III) spin crossover complexes
Authors: Sirirak Jitnapa , Sertphon Darunee , Phonsri Wasinee , Harding Phimphaka , Harding David J. 
Published: February 2017

AbstractA detailed investigation of the accuracy of different quantum mechanical methods for the study of iron(III) spin crossover complexes is presented. The energy spin state gap between the high and low spin states; ΔE(HS‐LS) of nine iron(III) quinolylsalicylaldiminate complexes were calculated with nine different DFT functionals, then compared. DFT functionals: B3LYP, B3LYP‐D3, B3LYP*, BH&HLYP, BP86, OLYP, OPBE, M06L, and TPSSh were tested with six basis sets: 3‐21G*, dgdzvp, 6‐31G**, cc‐pVDZ, Def2TZVP, and cc‐pVTZ. The cations from the X‐ray crystal structures of [Fe(qsal‐OMe)2]Cl·MeCN·H2O, [Fe(qsal‐OMe)2]Cl·2MeOH·0.5H2O, [Fe(qsal‐OMe)2]BF4·MeOH, [Fe(qsal‐OMe)2]NCS·CH2Cl2, [Fe(qsal‐F)2]NCS, [Fe(qsal‐Cl)2]NCS·MeOH, [Fe(qsal‐Br)2]NCS·MeOH, [Fe(qsal‐I)2]OTf·MeOH, and [Fe(qsal)2]NCS⋅CH2Cl2 were used as starting structures. The results show that B3LYP, B3LYP‐D3, OLYP, and OPBE with a 6‐31G**, Def2TZVP, and cc‐pVTZ basis set give reasonable results of ΔE(HS‐LS) compared with the experimental data. The enthalpy of [Fe(qsal‐I)2]+ calculated with an OLYP functional and cc‐pVTZ basis set (1.48 kcal/mol) most closely matches the experimental data (1.34 kcal/mol). B3LYP* yields an enthalpy of 5.92 kcal/mol suggesting it may be unsuitable for these Fe(III) complexes, mirroring recent results by Kepp (Inorg. Chem., 2016, 55, 2717–2727).
Design of donor–acceptor–donor (D–A–D) type small molecule donor materials with efficient photovoltaic parameters
Authors: Irfan Muhammad , Iqbal Javed , Sadaf Sana , Eliasson Bertil , Rana Usman Ali , Ud‐din Khan Salah , Ayub Khurshid 
Published: February 2017

AbstractFour Donor–Acceptor–Donor (D–A–D) type of donor molecules (M1‐M4) with triphenylamine (TPA) as donor moiety, thiophene as bridge, and thiazolothiazole as acceptor unit were designed and its photovoltaic parameters were equated with reference molecule “R.” DFT functional CAM‐B3LYP/6‐31G (d,p) was found best for geometry optimization and TD‐CAM‐B3LYP/6‐31G (d,p) was found suitable for excited state calculations. Among designed donor molecules, M4 manifests suitable lowest band gap of 4.73 eV, frontier molecular orbital energy levels as well as distinctive broad absorption of 455.3 nm due to the stronger electron withdrawing group. The electron‐withdrawing substituents contribute to red shifts of absorption spectra and better stabilities for designed molecules. The theoretically determined reorganization energies of designed donor molecules suggested excellent charge mobility property. The lower λe values in comparison with λh illustrated that these four donor materials would be ideal for electron transfer and M4 would be best amongst the investigated molecules with lowest λe of 0.0177. Furthermore, the calculated Voc of M4 is 2.04 V with respect to PC60BM (phenyl‐C61‐butyric acid methyl ester). This study revealed that the designed donor materials are suitable and recommended for high performance organic solar cell devices.