bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reproduction of motion artifacts for performance analysis of prospective motion correction in MRI
Authors: Herbst Michael , Maclaren Julian , Lovell‐Smith Cris , Sostheim Rebecca , Egger Karl , Harloff Andreas , Korvink Jan , Hennig Juergen , Zaitsev Maxim 
Published: February 2013

PurposeDespite numerous publications describing the ability of prospective motion correction to improve image quality in magnetic resonance imaging of the brain, a reliable approach to assess this improvement is still missing. A method that accurately reproduces motion artifacts correctable with prospective motion correction is developed, and enables the quantification of the improvements achieved.MethodsA software interface was developed to simulate rigid body motion by changing the scanning coordinate system relative to the object. Thus, tracking data recorded during a patient scan can be used to reproduce the prevented motion artifacts on a volunteer or a phantom. The influence of physiological motion on image quality was investigated by filtering these data. Finally, the method was used to reproduce and quantify the motion artifacts prevented in a patient scan.ResultsThe accuracy of the method was tested in phantom experiments and in vivo. The calculated quality factor, as well as a visual inspection of the reproduced artifacts shows a good correspondence to the original.ConclusionPrecise reproduction of motion artifacts assists qualification of prospective motion correction strategies. The presented method provides an important tool to investigate the effects of rigid body motion on a wide range of sequences, and to quantify the improvement in image quality through prospective motion correction. Magn Reson Med 71:182–190, 2014. © 2013 Wiley Periodicals, Inc.
Ex vivo MR volumetry of human brain hemispheres
Authors: Kotrotsou Aikaterini , Bennett David A. , Schneider Julie A. , Dawe Robert J. , Golak Tom , Leurgans Sue E. , Yu Lei , Arfanakis Konstantinos 
Published: February 2013

PurposeThe aims of this work were to (a) develop an approach for ex vivo MR volumetry of human brain hemispheres that does not contaminate the results of histopathological examination, (b) longitudinally assess regional brain volumes postmortem, and (c) investigate the relationship between MR volumetric measurements performed in vivo and ex vivo.MethodsAn approach for ex vivo MR volumetry of human brain hemispheres was developed. Five hemispheres from elderly subjects were imaged ex vivo longitudinally. All datasets were segmented. The longitudinal behavior of volumes measured ex vivo was assessed. The relationship between in vivo and ex vivo volumetric measurements was investigated in seven elderly subjects imaged both antemortem and postmortem.ResultsThis approach for ex vivo MR volumetry did not contaminate the results of histopathological examination. For a period of 6 months postmortem, within‐subject volume variation across time points was substantially smaller than intersubject volume variation. A close linear correspondence was detected between in vivo and ex vivo volumetric measurements.ConclusionRegional brain volumes measured with this approach for ex vivo MR volumetry remain relatively unchanged for a period of 6 months postmortem. Furthermore, the linear relationship between in vivo and ex vivo MR volumetric measurements suggests that this approach captures information linked to antemortem macrostructural brain characteristics. Magn Reson Med 71:364–374, 2014. © 2013 Wiley Periodicals, Inc.
Spiral trajectory design: A flexible numerical algorithm and base analytical equations
Authors: Pipe James G. , Zwart Nicholas R. 
Published: February 2013

PurposeSpiral‐based trajectories for magnetic resonance imaging can be advantageous, but are often cumbersome to design or create. This work presents a flexible numerical algorithm for designing trajectories based on explicit definition of radial undersampling, and also gives several analytical expressions for charactering the base (critically sampled) class of these trajectories.Theory and MethodsExpressions for the gradient waveform, based on slew and amplitude limits, are developed such that a desired pitch in the spiral k‐space trajectory is followed. The source code for this algorithm, written in C, is publicly available. Analytical expressions approximating the spiral trajectory (ignoring the radial component) are given to characterize measurement time, gradient heating, maximum gradient amplitude, and off‐resonance phase for slew‐limited and gradient amplitude‐limited cases. Several numerically calculated trajectories are illustrated, and base Archimedean spirals are compared with analytically obtained results.ResultsSeveral different waveforms illustrate that the desired slew and amplitude limits are reached, as are the desired undersampling patterns, using the numerical method. For base Archimedean spirals, the results of the numerical and analytical approaches are in good agreement.ConclusionA versatile numerical algorithm was developed, and was written in publicly available code. Approximate analytical formulas are given that help characterize spiral trajectories. Magn Reson Med 71:278–285, 2014. © 2013 Wiley Periodicals, Inc.
Orthogonalizing crusher and diffusion‐encoding gradients to suppress undesired echo pathways in the twice‐refocused spin echo diffusion sequence
Authors: Nagy Zoltán , Thomas David L. , Weiskopf Nikolaus 
Published: February 2013

PurposeThe twice‐refocused spin echo sequence is widely used in diffusion imaging due to its excellent performance in reducing eddy currents. The three radio frequency pulses give rise to eight separate signal pathways. Because there is no general solution for the size and arrangement for crusher gradients, with constant size and orientation, that is effective for all arbitrary diffusion‐sensitizing b‐values and directions, this article introduces and validates a solution whereby the crusher and diffusion‐encoding gradients are always kept orthogonal, thus ensuring their independence.MethodsThe cancellation of the crusher and diffusion gradients was demonstrated. Subsequently, crusher gradients were implemented in such a way that they were always orthogonal to the diffusion gradient. Phantom and in‐vivo experiments were performed to ascertain that orthogonally implemented crusher gradients alleviate the problem without lowering image quality.ResultsIn all experiments, when the crusher gradients' action was cancelled by the diffusion‐encoding gradients artifactual signal modulation was observed. When orthogonal gradients were implemented the artifacts were eliminated without detrimental effects on image quality.ConclusionsOrthogonal crushers are easy to implement and can be used for any variant of diffusion imaging sequences (e.g., diffusion tensor imaging, fiber diameter mapping) where the twice‐refocused scheme is used. Magn Reson Med 71:506–515, 2014. © 2013 Wiley Periodicals, Inc.
Whole‐body and local RF absorption in human models as a function of anatomy and position within 1.5T MR body coil
Authors: Murbach Manuel , Neufeld Esra , Kainz Wolfgang , Pruessmann Klaas P. , Kuster Niels 
Published: February 2013

PurposeRadiofrequency energy deposition in magnetic resonance imaging must be limited to prevent excessive heating of the patient. Correlations of radiofrequency absorption with large‐scale anatomical features (e.g., height) are investigated in this article.Theory and MethodsThe specific absorption rate (SAR), as the pivotal parameter for quantifying absorbed radiofrequency, increases with the radial dimension of the patient and therefore with the large‐scale anatomical properties. The absorbed energy in six human models has been modeled in different Z‐positions (head to knees) within a 1.5T bodycoil.ResultsFor a fixed
incident field, the whole‐body SAR can be up to 2.5 times higher (local SAR up to seven times) in obese adult models compared to children. If the exposure is normalized to 4 W/kg whole‐body SAR, the local SAR can well‐exceed the limits for local transmit coils and shows intersubject variations of up to a factor of three.ConclusionsThe correlations between anatomy and induced local SAR are weak for normalized exposure, but strong for a fixed
field, suggesting that anatomical properties could be used for fast SAR predictions. This study demonstrates that a representative virtual human population is indispensable for the investigation of local SAR levels. Magn Reson Med 71:839–845, 2014. © 2013 Wiley Periodicals, Inc.
PLANNING AND PARTICIPATION IN CITIES THAT MOVE: IDENTIFYING OBSTACLES TO MUNICIPAL MOBILITY MANAGEMENT
Authors: Landau Loren B. , Segatti Aurelia , Misago Jean Pierre 
Published: February 2013

SUMMARYThe dual processes of rapidly transforming cities and administrative decentralisation demands that local government address human mobility as a means of countering urban poverty. Despite this imperative, local authorities are often poorly equipped to address the needs of poor and transient residents. Through an examination of four South African municipalities, this article helps to identify three critical factors working against effective responses: poor data and conceptual bias; institutional ambiguities and budgeting processes; and, ironically, participatory planning. Although any one of these could serve as a basis for an article, by taking them together, we better summarise the challenges' scope and outline areas for further research and policy intervention. The article concludes by considering these findings' practical and scholarly implications. Copyright © 2013 John Wiley & Sons, Ltd.
SIOP PODC: Recommendations for supportive care of children with cancer in a low‐income setting
Authors: Israels Trijn , Renner Lorna , Hendricks Marc , Hesseling Peter , Howard Scott , Molyneux Elizabeth 
Published: February 2013

AbstractThese supportive care recommendations were prepared to guide doctors who practice in areas with significantly limited resources but who have sufficient infrastructure and training to treat children with cancer with curative intent. The success of any cancer treatment regimen depends largely on the availability and quality of supportive care and this also determines the intensity of treatment that can be delivered. We present practical recommendations on how to prevent infections, general nursing care, management of febrile neutropenia, nutritional assessment and support, treatment of co‐infections and the social support to help prevent failure to complete treatment in resource poor settings. Pediatr Blood Cancer 2013; 60: 899–904. © 2013 Wiley Periodicals, Inc.
Determination of Endogenous Brassinosteroids in Plant Tissues Using Solid‐phase Extraction with Double Layered Cartridge Followed by High‐performance Liquid Chromatography–Tandem Mass Spectrometry
Authors: Ding Jun , Mao Li‐Jing , Wang Shao‐Ting , Yuan Bi‐Feng , Feng Yu‐Qi 
Published: February 2013

ABSTRACTIntroductionBrassinosteroids (BRs) are a group of important phytohormones that play vital roles in plant growth, development and a series of physiological phenomena. In order to understand biosynthesis, degradation and metabolic pathways of BRs, a reliable analytical method of BRs with effective sample pre‐treatment process is favourable.ObjectiveThe development of a quick and effective method for the quantification of endogenous BRs in plant tissue with the aid of double layered solid‐phase extraction (SPE) cartridges (graphite carbon black and primary secondary amine silica sorbent: GCB/PSA).MethodThe method involved an initial extraction of BRs with acetonitrile, a dehydration process with anhydrous MgSO4 and NaCl, a SPE purification process with a double layered cartridge, and a further clean‐up step utilising liquid–liquid extraction (LLE). The purification process was mainly realised on the GCB/PSA cartridge. GCB could eliminate hydrophobic compounds, especially those containing a π system, and PSA was introduced to remove the polar interferences. Endogenous BRs were quantified by HPLC–ESI–MS/MS.ResultsGood linearities were obtained in the range of 0.4–500 ng/mL (0.0124–15 ng), with the correlation coefficients above 0.9957. The relative recoveries of BRs of this method were in the range of 71.1–113.1%, with intra‐ and interday relative standard deviations (RSDs) less than 16.3%. With the proposed method, the requirement of plant tissue amount was minimised to 1 g fresh weight, which is the smallest amount reported so far, to our knowledge. Copyright © 2013 John Wiley & Sons, Ltd.
Comparative effectiveness research using electronic health records: impacts of oral antidiabetic drugs on the development of chronic kidney disease
Authors: L. Masica Andrew , Ewen Edward , A. Daoud Yahya , Cheng Dunlei , Franceschini Nora , E. Kudyakov Rustam , R. Bowen James , Brouwer Emily S. , Wallace Dennis , S. Fleming Neil , West Suzanne L. 
Published: February 2013

ABSTRACTPurposeLittle is known about the comparative effects of common oral antidiabetic drugs ([OADs] metformin, sulfonylureas, or thiazolidinediones [THZs]) on chronic kidney disease (CKD) outcomes in patients newly diagnosed with type 2 diabetes (T2DM) and followed in community primary care practices. Electronic health records (EHRs) were used to evaluate the relationships between OAD class use and incident proteinuria and prevention of glomerular filtration rate decline.MethodsA retrospective cohort study on newly diagnosed T2D cases requiring OADs documented in the EHRs of two primary care networks between 1998 and 2009 was conducted. CKD outcomes were new‐onset proteinuria and estimated GFR (eGFR) falling below 60 ml/min/1.73 m2. OAD exposures defined cohorts. Hazard ratios represent differential CKD outcome risk per year of OAD class use.ResultsA total of 798 and 977 patients qualified for proteinuria and eGFR outcome analyses, respectively. With metformin as the reference group, sulfonylurea exposure trended toward association with an increased risk of developing proteinuria ([adjusted hazard ratio; 95% CI] 1.27; 0.93, 1.74); proteinuria risk associated with THZ exposure (1.00; 0.70, 1.42) was similar to metformin. Compared with metformin, sulfonylurea exposure was associated with an increased risk of eGFR reduction to <60 ml/min/1.73 m2 (1.41; 1.05, 1.91). THZ exposure (1.04; 0.71, 1.50) was not associated with change in the risk of eGFR decline.ConclusionsIn a primary care population, metformin appeared to decrease the risk of CKD development compared with sulfonlyureas; risks of CKD development between metformin and THZs were similar. EHR use in pharmacotherapy comparative effectiveness research creates specific challenges and study limitations. Copyright © 2013 John Wiley & Sons, Ltd.
Insight into the sporulation phosphorelay: Crystal structure of the sensor domain of Bacillus subtilis histidine kinase, KinD
Authors: Wu R. , Gu M. , Wilton R. , Babnigg G. , Kim Y. , Pokkuluri P. R. , Szurmant H. , Joachimiak A. , Schiffer M. 
Published: February 2013

AbstractThe Bacillus subtilis KinD signal‐transducing histidine kinase is a part of the sporulation phosphorelay known to regulate important developmental decisions such as sporulation and biofilm formation. We have determined crystal structures of the extracytoplasmic sensing domain of KinD, which was copurified and crystallized with a pyruvate ligand. The structure of a ligand‐binding site mutant was also determined; it was copurified and crystallized with an acetate ligand. The structure of the KinD extracytoplasmic segment is similar to that of several other sensing domains of signal transduction proteins and is composed of tandem Per‐Arnt‐Sim (PAS)‐like domains. The KinD ligand‐binding site is located on the membrane distal PAS‐like domain and appears to be highly selective; a single mutation, R131A, abolishes pyruvate binding and the mutant binds acetate instead. Differential scanning fluorimetry, using a variety of monocarboxylic and dicarboxylic acids, identified pyruvate, propionate, and butyrate but not lactate, acetate, or malate as KinD ligands. A recent report found that malate induces biofilm formation in a KinD‐dependent manner. It was suggested that malate might induce a metabolic shift and increased secretion of the KinD ligand of unknown identity. The structure and binding assays now suggests that this ligand is pyruvate and/or other small monocarboxylic acids. In summary, this study gives a first insight into the identity of a molecular ligand for one of the five phosphorelay kinases of B. subtilis.
Nucleophosmin mutations in acute myeloid leukemia: A tale of protein unfolding and mislocalization
Authors: Federici Luca , Falini Brunangelo 
Published: February 2013

AbstractNucleophosmin (NPM1) is an abundant, ubiquitously expressed protein mainly localized at nucleoli but continuously shuttling between nucleus and cytoplasm. NPM1 plays a role in several cellular functions, including ribosome biogenesis and export, centrosome duplication, chromatin remodeling, DNA repair, and response to stress stimuli. Much of the interest in this protein arises from its relevance in human malignancies. NPM1 is frequently overexpressed in solid tumors and is the target of several chromosomal translocations in hematologic neoplasms. Notably, NPM1 has been characterized as the most frequently mutated gene in acute myeloid leukemia (AML). Mutations alter the C‐terminal DNA‐binding domain of the protein and result in its aberrant nuclear export and stable cytosolic localization. In this review, we focus on the leukemia‐associated NPM1 C‐terminal domain and describe its structure, function, and the effect exerted by leukemic mutations. Finally, we discuss the possibility to target NPM1 for the treatment of cancer and, in particular, of AML patients with mutated NPM1 gene.
Transverse vibration bandgaps in phononic‐crystal Euler beams on a Winkler foundation studied by a modified transfer matrix method
Authors: Zhang Yan , Han Lin , Jiang Lin‐hua 
Published: February 2013

AbstractIn this paper, a modified transfer matrix method is proposed to solve the transverse vibration bandgaps (BGs) in phononic crystal (PC) Euler beams on a Winkler foundation. An equivalent critical frequency is introduced to facilitate the calculation of the end frequency of the first BG. The band structures of a lead–steel PC Euler beam either on a Winkler foundation or not show that the existence of a foundation has a significant influence on the distribution of BGs. A new BG that starts at 0 Hz appears. Additional results demonstrate that a very narrow passband could exist between the first two BGs. This study is aimed at searching for large BGs, especially at low frequencies. magnified imageBand structures for the lead–steel PC Euler beam on a Winkler foundation (continuous line) or not (dash line). A new BG that starts at 0 Hz appears in the case of having a foundation.
Acquisition parameters optimization of a transmission electron forward scatter diffraction system in a cold‐field emission scanning electron microscope for nanomaterials characterization
Authors: Brodusch Nicolas , Demers Hendrix , Trudeau Michel , Gauvin Raynald 
Published: February 2013

SummaryTransmission electron forward scatter diffraction (t‐EFSD) is a new technique providing crystallographic information with high resolution on thin specimens by using a conventional electron backscatter diffraction (EBSD) system in a scanning electron microscope. In this study, the impact of tilt angle, working distance, and detector distance on the Kikuchi pattern quality were investigated in a cold‐field emission scanning electron microscope (CFE‐SEM). We demonstrated that t‐EFSD is applicable for tilt angles ranging from −20° to −40°. Working distance (WD) should be optimized for each material by choosing the WD for which the EBSD camera screen illumination is the highest, as the number of detected electrons on the screen is directly dependent on the scattering angle. To take advantage of the best performances of the CFE‐SEM, the EBSD camera should be close to the sample and oriented towards the bottom to increase forward scattered electron collection efficiency. However, specimen chamber cluttering and beam/mechanical drift are important limitations in the CFE‐SEM used in this work. Finally, the importance of t‐EFSD in materials science characterization was illustrated through three examples of phase identification and orientation mapping. SCANNING 35:375–386, 2013. © 2013 Wiley Periodicals, Inc.
Penetration resistance: A new approach to the energetics of indentations
Authors: Kaupp Gerd 
Published: February 2013

SummaryThis article deals with quantitative applications of the penetration resistance of experimental indentation loading curves without fittings or simulations in terms of the various energetic contributions for an improved understanding. The total applied work upon indentation with pyramids, cones and also spheres is partitioned between the indentation and the long‐range effects including friction in a constant 80/20 ratio for mathematical reasons and thus for all of the diverse materials and methods. Long‐range effects such as molecular migrations, rosettes, shear‐bands, pile‐up, sink‐in, and elastic stress are recalled. An easy integration of (higher) parabolas with known exponent is presented. The constant ratios of applied work, indentation work, and long‐range work allow for separation of surface effect work, reliable calculations of adhesion energies, and phase transformation energies. Corrections of Sneddon/Love and of Johnson, Kendall, Roberts (JKR) derived equations are now required. SCANNING 35:392–401, 2013. © 2013 Wiley Periodicals, Inc.
An exploratory study of the evolution of communicated information about the execution of large software systems
Authors: Shang Weiyi , Jiang Zhen Ming , Adams Bram , Hassan Ahmed E. , Godfrey Michael W. , Nasser Mohamed , Flora Parminder 
Published: February 2013

SUMMARYSubstantial research in software engineering focuses on understanding the dynamic nature of software systems in order to improve software maintenance and program comprehension. This research typically makes use of automated instrumentation and profiling techniques after the fact, that is, without considering domain knowledge. In this paper, we examine another source of dynamic information that is generated from statements that have been inserted into the code base during development to draw the system administrators' attention to important run‐time phenomena. We call this source communicated information (CI). Examples of CI include execution logs and system events. The availability of CI has sparked the development of an ecosystem of Log Processing Apps (LPAs) that surround the software system under analysis to monitor and document various run‐time constraints. The dependence of LPAs on the timeliness, accuracy and granularity of the CI means that it is important to understand the nature of CI and how it evolves over time, both qualitatively and quantitatively. Yet, to our knowledge, little empirical analysis has been performed on CI and its evolution. In a case study on two large open source and one industrial software systems, we explore the evolution of CI by mining the execution logs of these systems and the logging statements in the source code. Our study illustrates the need for better traceability between CI and the LPAs that analyze the CI. In particular, we find that the CI changes at a high rate across versions, which could lead to fragile LPAs. We found that up to 70% of these changes could have been avoided and the impact of 15% to 80% of the changes can be controlled through the use of robust analysis techniques by LPAs. We also found that LPAs that track implementation‐level CI (e.g. performance analysis) and the LPAs that monitor error messages (system health monitoring) are more fragile than LPAs that track domain‐level CI (e.g. workload modelling), because the latter CI tends to be long‐lived. Copyright © 2013 John Wiley & Sons, Ltd.