bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accumulation of promutagenic DNA adducts in the mouse distal colon after consumption of heme does not induce colonic neoplasms in the western diet model of spontaneous colorectal cancer
Authors: Winter Jean , Young Graeme P. , Hu Ying , Gratz Silvia W. , Conlon Michael A. , Le Leu Richard K. 
Published: October 2013

ScopeRed meat is considered a risk factor for colorectal cancer (CRC). Heme is considered to promote colonic hyperproliferation and cell damage. Resistant starch (RS) is a food that ferments in the colon with studies demonstrating protective effects against CRC. By utilizing the western diet model of spontaneous CRC, we determined if feeding heme (as hemin chloride) equivalent to a high red meat diet would increase colonic DNA adducts and CRC and whether RS could abrogate such effects.Methods and resultsFour groups of mice: control, heme, RS and heme + RS were fed diets for 1 or 18 months. Colons were analyzed for apoptosis, proliferation, DNA adducts “8‐hydroxy‐2‐deoxyguanosine” and “O6‐methyl‐2‐deoxyguanosine” (O6MeG), and neoplasms. In the short term, heme increased cell proliferation (p < 0.05). Changes from 1 to 18 months showed increased cell proliferation (p < 0.01) and 8‐hydroxy‐2‐deoxyguanosine adducts (p < 0.05) in all groups, but only heme‐fed mice showed reduced apoptosis (p < 0.01) and increased O6MeG adducts (p < 0.01). The incidence of colon neoplasms was not different between any interventions.ConclusionWe identified heme to increase proliferation in the short term, inhibit apoptosis over the long term, and increase O6MeG adducts in the colon over time although these changes did not affect colonic neoplasms within this mouse model.
Propagation of calibration errors in prospective motion correction using external tracking
Authors: Zahneisen Benjamin , Keating Brian , Ernst Thomas 
Published: October 2013

PurposeProspective motion correction of MRI scans using an external tracking device (such as a camera) is becoming increasingly popular, especially for imaging of the head. In order for external tracking data to be transformed into the MR scanner reference frame, the pose (i.e., position and orientation) of the camera relative to the scanner—or cross‐calibration—must be accurate. In this study, we investigated how errors in cross‐calibration affect the accuracy of motion correction feedback in MRI.Theory and MethodsAn operator equation is derived describing how calibration errors relate to errors in applied motion compensation. By taking advantage of spherical symmetry and performing a Taylor approximation for small rotation angles, a closed form expression and upper limit for the residual tracking error is provided.ResultsExperiments confirmed theoretical predictions of a bilinear dependence of the residual rotational component on the calibration error and the motion performed, modulated by a sinusoidal dependence on the angle between the calibration error axis and motion axis. The residual translation error is bounded by the sum of the rotation angle multiplied by the translational calibration error plus the linear head displacement multiplied by the calibration error angle.ConclusionThe results make it possible to calculate the required cross‐calibration accuracy for external tracking devices for a range of motions. Scans with smaller expected movements require less accuracy in cross‐calibration than scans involving larger movements. Typical clinical applications require that the calibration accuracy is substantially below 1 mm and 1°. Magn Reson Med 72:381–388, 2014. © 2013 Wiley Periodicals, Inc.
Development of an MRI phantom for diffusion‐weighted imaging with independent adjustment of apparent diffusion coefficient values and T2 relaxation times
Authors: Gatidis Sergios , Schmidt Holger , Martirosian Petros , Schwenzer Nina F. 
Published: October 2013

PurposeTo design a phantom for diffusion‐weighted imaging (DWI) with defined apparent diffusion coefficients (ADC) and T2 relaxation times.MethodsVarying concentrations of polyethylene glycol (PEG) were used for the adjustment of diffusivity. T2 relaxation times were tuned by adding of the MR contrast agent gadobutrol. Relaxation times and apparent diffusion coefficients were quantified using a multiecho spin echo sequence and an echo planar imaging (EPI) DWI sequence, respectively, on a 3T clinical scanner.ResultsIncreasing concentrations of PEG led to a marked impairment of diffusivity accompanied by only moderate changes of T2 relaxation times. Adding gadobutrol to the PEG solutions allowed for adjustment of transverse relaxation times to predefined values. Thus, a broad range of defined ADC values and T2 relaxation times could be accurately achieved in the final phantom.ConclusionThe proposed phantom allows for standardized in vitro studies of DWI methods and protocols. The obtained MR image contrasts are similar to a variety of biological tissues, which can contribute to optimization of imaging techniques with respect to specific clinical questions. Due to the simplicity of design and the accessibility of the contained compounds, this phantom may also serve as a tool for standardization and calibration. Magn Reson Med 72:459–463, 2014. © 2013 Wiley Periodicals, Inc.
Quantitative T2 mapping of the mouse heart by segmented MLEV phase‐cycled T2 preparation
Authors: Coolen Bram F. , Simonis Frank F.J. , Geelen Tessa , Moonen Rik P.M. , Arslan Fatih , Paulis Leonie E.M. , Nicolay Klaas , Strijkers Gustav J. 
Published: October 2013

PurposeA high‐quality, reproducible, multi‐slice T2‐mapping protocol for the mouse heart is presented.MethodsA T2‐prepared sequence with composite 90° and 180° radiofrequency pulses in a segmented MLEV phase cycling scheme was developed. The T2‐mapping protocol was optimized using simulations and evaluated with phantoms.ResultsRepeatability for determination of myocardial T2 values was assessed in vivo in n = 5 healthy mice on 2 different days. The average baseline T2 of the left ventricular myocardium was 22.5 ± 1.7 ms. The repeatability coefficient for R2 = 1/T2 for measurements at different days was ΔR2 = 6.3 s−1. Subsequently, T2 mapping was applied in comparison to late‐gadolinium‐enhancement (LGE) imaging, to assess 1‐day‐old ischemia/reperfusion (IR) myocardial injury in n = 8 mice. T2 in the infarcts was significantly higher than in remote tissue, whereas remote tissue was not significantly different from baseline. Infarct sizes based on T2 versus LGE showed strong correlation. To assess the time‐course of T2 changes in the infarcts, T2 mapping was performed at day 1, 3, and 7 after IR injury in a separate group of mice (n = 16). T2 was highest at day 3, in agreement with the expected time course of edema formation and resolution after myocardial infarction.ConclusionT2 prepared imaging provides high quality reproducible T2 maps of healthy and diseased mouse myocardium. Magn Reson Med 72:409–417, 2014. © 2013 Wiley Periodicals, Inc.
Compressed sensing of spatial electron paramagnetic resonance imaging
Authors: Johnson David H. , Ahmad Rizwan , He Guanglong , Samouilov Alexandre , Zweier Jay L. 
Published: October 2013

PurposeTo improve image quality and reduce data requirements for spatial electron paramagnetic resonance imaging (EPRI) by developing a novel reconstruction approach using compressed sensing (CS).MethodsEPRI is posed as an optimization problem, which is solved using regularized least‐squares with sparsity promoting penalty terms, consisting of the l1 norms of the image itself and the total variation of the image. Pseudo‐random sampling was employed to facilitate recovery of the sparse signal. The reconstruction was compared with the traditional filtered back‐projection reconstruction for simulations, phantoms, isolated rat hearts, and mouse gastrointestinal (GI) tracts labeled with paramagnetic probes.ResultsA combination of pseudo‐random sampling and CS was able to generate high‐fidelity EPR images at high acceleration rates. For three‐dimensional (3D) phantom imaging, CS‐based EPRI showed little visual degradation at nine‐fold acceleration. In rat heart datasets, CS‐based EPRI produced high quality images with eight‐fold acceleration. A high resolution mouse GI tract reconstruction demonstrated a visual improvement in spatial resolution and a doubling in signal‐to‐noise ratio (SNR).ConclusionA novel 3D EPRI reconstruction using compressed sensing was developed and offers superior SNR and reduced artifacts from highly undersampled data. Magn Reson Med 72:893–901, 2014. © 2013 Wiley Periodicals, Inc.
Multiparametric optical and MR imaging demonstrate inhibition of tumor angiogenesis natural history by mural cell therapy
Authors: Faye Nathalie , Clément Olivier , Balvay Daniel , Fitoussi Victor , Pidial Laetitia , Sandoval Federico , Autret Gwennhael , Silvestre Jean Sébastien , Dean Carole Leré , Alison Marianne , Fournier Laure S. 
Published: October 2013

PurposeTo determine whether functional imaging using MRI and fibered confocal fluorescence microscopy (FCFM) could be used to monitor cell therapy by mural progenitor cells (MPC).MethodsFifty mice bearing TC1 murine xenograft tumors were allocated into: control (n = 17), sham (phosphate buffer saline, n = 16), and MPC‐treated (MPC, n = 17) groups. MRI was performed before (D0) and 7 days (D7) after injection measuring tumor size, R2* under air, oxygen, and carbogen using blood oxygen level dependent (BOLD) and f (fraction linked to microcirculation), D* (perfusion related coefficient) and Dr (restricted diffusion coefficient) using diffusion‐weighted sequences based on the IVIM (intravoxel incoherent motion) method. FCFM was performed at D7 measuring “index leakage” (capillary permeability).ResultsTumor growth was significantly slowed down in the MPC‐treated animals (P = 0.002) on D7. R2*air significantly decreased in controls between D0 and D7 (P = 0.03), reflecting a decrease in tumor oxygenation. ΔR2*O2CO2 significantly increased in controls between D0 and D7 (P = 0.01) reflecting loss of vessel response to carbogen. D* significantly decreased in controls between D0 and D7 (P = 0.03). Finally, “index leakage” was lower in the MPC‐treated tumors (P = 0,009).ConclusionTreatment by MPC resulted in slowing down of tumor growth, capillary permeability decrease, and stabilization of tumor angiogenesis. Magn Reson Med 72:841–849, 2014. © 2013 Wiley Periodicals, Inc.
Spiral tissue phase velocity mapping in a breath‐hold with non‐cartesian SENSE
Authors: Simpson Robin , Keegan Jennifer , Gatehouse Peter , Hansen Michael , Firmin David 
Published: October 2013

PurposeTissue phase velocity mapping (TPVM) is capable of reproducibly measuring regional myocardial velocities. However acquisition durations of navigator gated techniques are long and unpredictable while current breath‐hold techniques have low temporal resolution. This study presents a spiral TPVM technique which acquires high resolution data within a clinically acceptable breath‐hold duration.MethodsTen healthy volunteers are scanned using a spiral sequence with temporal resolution of 24 ms and spatial resolution of 1.7 × 1.7 mm. Retrospective cardiac gating is used to acquire data over the entire cardiac cycle. The acquisition is accelerated by factors of 2 and 3 by use of non‐Cartesian SENSE implemented on the Gadgetron GPU system resulting in breath‐holds of 17 and 13 heartbeats, respectively. Systolic, early diastolic, and atrial systolic global and regional longitudinal, circumferential, and radial velocities are determined.ResultsGlobal and regional velocities agree well with those previously reported. The two acceleration factors show no significant differences for any quantitative parameter and the results also closely match previously acquired higher spatial resolution navigator‐gated data in the same subjects.ConclusionBy using spiral trajectories and non‐Cartesian SENSE high resolution, TPVM data can be acquired within a clinically acceptable breath‐hold. Magn Reson Med 72:659–668, 2014. © 2013 Wiley Periodicals, Inc.
Protein expression profiling during wallerian degeneration after rat sciatic nerve injury
Authors: Li Meiyuan , Zhang Pingan , Guo Weimin , Li Huaiqin , Gu Xiaosong , Yao Dengbing 
Published: October 2013

ABSTRACTIntroduction: Wallerian degeneration (WD) is an important area of research in modern neuroscience. Many protein expressions are regulated by differentially expressed genes in WD, but the precise mechanisms are elusive. Methods: In this study, we profiled differentially expressed proteins in WD after rat sciatic nerve injury using an antibody array. Results: Functional analysis positively identified cell proliferation, regulation of cell proliferation, and immune system processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed molecular networks related mainly to cytokine–cytokine receptor interaction, the mitogen‐activated proteinkinase (MAPK) signaling pathway, apoptosis, the toll‐like receptor (TLR) signaling pathway, and the Janus kinase (Jak) ‐ signal transducer and activator of transcription (STAT) signaling pathway. Interactions between these differential proteins were well established and regulated by the key factors transforming growth factor beta 1 (TGF‐β1), toll‐like receptor 4 (TLR4), Fas ligand (FasL), and 5′‐AMP‐activated protein kinase catalytic subunit alpha‐1 (PRKAA1). Conclusions: These results provide information related to functional analysis of differentially expressed genes during WD. Muscle Nerve 50: 73–78, 2014
Shifts in EMG spectral power during fatiguing dynamic contractions
Authors: Beck Travis W. , Stock Matt S. , Defreitas Jason M. 
Published: October 2013

ABSTRACTIntroduction: We examined the etiology of the electromyographic (EMG) spectral shift during dynamic fatigue. Methods: Nineteen subjects (mean ± SD age = 22.4 ± 1.6 years) performed 50 consecutive maximal concentric isokinetic contractions of dominant leg extensors. Surface EMG signals were detected from the vastus lateralis, rectus femoris, and vastus medialis during each contraction, processed with a wavelet analysis, and the resulting spectra were decomposed with a nonparametric spectral decomposition procedure. Results: The results indicated that the decreases in EMG frequency during the 50 contractions were generally due to reductions in high‐frequency power and increases in low‐frequency power. In addition, the spectral shifts were most pronounced for the rectus femoris, followed by the vastus lateralis, and then the vastus medialis. Conclusions: The spectral decomposition procedure is much more sensitive for tracking dynamic fatigue than is EMG mean frequency or median frequency. Muscle Nerve 50: 95–102, 2014
Dynamic analysis of strain localization in water‐saturated clay using a cyclic elasto‐viscoplastic model
Authors: Shahbodagh Khan B. , Mirjalili M. , Kimoto S. , Oka F. 
Published: October 2013

SUMMARYA computational framework is presented for dynamic strain localization and deformation analyses of water‐saturated clay by using a cyclic elasto‐viscoplastic constitutive model. In the model, the nonlinear kinematic hardening rule and softening due to the structural degradation of soil particles are considered. In order to appropriately simulate the large deformation phenomenon in strain localization analysis, the dynamic finite element formulation for a two‐phase mixture is derived in the updated Lagrangian framework. The shear band development is shown through the distributions of viscoplastic shear strain, the axial strain, the mean effective stress, and the pore water pressure in a normally consolidated clay specimen. From the local stress–strain relations, more brittleness is found inside the shear bands than outside of them. The effects of partially drained conditions and mesh‐size dependency on the shear banding are also investigated. The effect of a partially drained boundary is found to be insignificant on the dynamic shear band propagation because of the rapid rate of applied loading and low permeability of the clay. Using the finer mesh results in slightly narrower shear bands; nonetheless, the results manifest convergency through the mesh refinement in terms of the overall shape of shear banding and stress–strain relations. Copyright © 2013 John Wiley & Sons, Ltd.
Modeling progressive failures in rock slopes with non‐persistent joints using the numerical manifold method
Authors: An Xinmei , Ning Youjun , Ma Guowei , He Lei 
Published: October 2013

SUMMARYRock slope failure is a complex process that usually involves both opening/sliding along pre‐existing discontinuities as well as fracturing of intact rock bridges. Discontinuity persistence is an important factor governing rock slope instabilities. However, traditional slope failure analysis assumes persistent discontinuities, and rock slope fails along a predefined persistent continuous potential failure surface because of the limitations of the analysis tools. This paper proposes the numerical manifold method (NMM) incorporated with a Mohr–Coulomb criterion‐based fracturing algorithm to simulate the progressive failure of rock slopes with non‐persistent joints. Detailed fracturing algorithm is first presented. Then, the NMM enabling fracturing is calibrated through simulating an edge‐cracked plate and the Brazilian test. Lastly, the developed code is applied to investigate the failure process of rock slopes involving non‐persistent joints. Numerical results indicate that the proposed method can capture the opening/sliding along existing discontinuities, the fracturing in intact rock bridges and the final kinematic release. Progressive slope failure is well exhibited. Copyright © 2013 John Wiley & Sons, Ltd.
Bounding surface SANICLAY plasticity model for cyclic clay behavior
Authors: Seidalinov Gaziz , Taiebat Mahdi 
Published: October 2013

SUMMARYNatural clays are anisotropic in their in situ state and have an undisturbed shear strength in excess of the remolded strength. In addition, most of the structures founded on clay deposits must be designed to withstand cyclic loads such as earthquakes or ocean waves. When subjected to cyclic loadings, clay exhibits complex response. A realistic modeling of clay response under irregular loading requires an appropriate description of the stress‐strain relationship. This paper extends the formulation of a Simple ANIsotropic CLAY plasticity (SANICLAY) model by incorporation of a bounding surface formulation for simulation of clay response under cyclic loading. The most important elements of the proposed formulation are incorporation of bounding surface plasticity concept with proper repositioning of the projection center and adoption of a new damage parameter. These have led to significantly improved simulation of clay response in cyclic loading. The model is developed with the aim of maintaining the simplicity and yet including an adequate level of sophistication for successful modeling of the key features of clay response. The formulation is presented in detail followed by validation of the model demonstrating its capabilities in capturing a number of important characteristic features of clay response in cyclic loading. Copyright © 2013 John Wiley & Sons, Ltd.
Fast algorithms for convex cost flow problems on circles, lines, and trees
Authors: Orlin James B. , Vaidyanathan Balachandran 
Published: October 2013

AbstractWe develop efficient algorithms to solve convex cost flow problems where the underlying graph is a circle, a line, or a tree. Each node i has an associated supply/demand b( i). The cost of sending flow on arc ( i, j) is a piecewise linear convex function fij defined over . Let n be the number of nodes and m = O(n) be the total number of pieces of all the convex functions. A flow x is feasible if the imbalances on all nodes are nonnegative. Excess stored on node i has an associated linear cost . We show that the problem on a circle can be transformed into an equivalent problem on a line in O( n) time. Thereafter, we develop an algorithm that solves the problem on a line in time, where sort( n) is the time to sort n real numbers and is the inverse Ackermann function. We also prove that when the nodes lie on a tree, the problem can be solved in time using the dynamic tree data structure. We describe applications in areas such as distributed computing, lot‐sizing, computational biology, computational music, and transportation. © 2013 Wiley Periodicals, Inc. NETWORKS, Vol. 62(4), 288–296 2013
The multi‐commodity pickup‐and‐delivery traveling salesman problem
Authors: Hernández‐Pérez Hipólito , Salazar‐González Juan‐José 
Published: October 2013

Abstract–The “multi‐commodity Pickup‐and‐Delivery Traveling Salesman Problem” (m‐PDTSP) is a generalization of the well‐known “Traveling Salesman Problem” in which cities correspond to customers providing or requiring known amounts of m different products, and the vehicle has a known capacity. Each customer must be visited exactly once by the vehicle serving the demands of the different products while minimizing the total travel distance. It is assumed that a unit of a product collected from a customer can be supplied to any other customer that requires this product. We introduce a mixed integer linear programming model for the m‐PDTSP, discuss a classical decomposition technique, describe valid inequalities to strengthen the linear programming relaxation of the model, and detail separation procedures to develop a branch‐and‐cut procedure. Computational experiments on randomly generated instances with up to 30 customers, three products, and small vehicle capacities are analyzed. © 2013 Wiley Periodicals, Inc. NETWORKS, Vol. 63(1), 46–59 2014
A template‐based adaptive large neighborhood search for the consistent vehicle routing problem
Authors: Kovacs Attila A. , Parragh Sophie N. , Hartl Richard F. 
Published: October 2013

Abstract–The importance of customer satisfaction was identified by many industries as a key factor of competitive advantage. So, for companies in the small package shipping industry, it can be reasonable to increase the service quality even at the expense of transportation cost to gain customer loyalty. These companies noticed that customer satisfaction can be increased by providing consistent service in the form of visiting customers with the same driver at approximately the same time of the day over a certain time period. Motivated by this real‐world problem, the consistent vehicle routing problem (ConVRP) combines traditional vehicle routing constraints with the requirements for service consistency. This article presents a fast solution method called template‐based adaptive large neighborhood search for the described problem. Compared to state‐of‐the‐art heuristics, the developed algorithm is highly competitive on the available benchmark instances. Additionally, new test instances are provided. These seem to be more challenging due to the variation of different model parameters and consequently help to identify interesting effects. Finally, a relaxed variant of the original ConVRP is presented. In this variant, the departure times from the depot can be delayed to adjust the service times of the customers. Experiments show that allowing later departure times considerably improves the solution quality under tight consistency requirements. © 2013 Wiley Periodicals, Inc. NETWORKS, Vol. 63(1), 60–81 2014