bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monitoring of release of cargo from nanocarriers by MRI/MR spectroscopy (MRS): Significance of T2/T effect of iron particles
Authors: Kato Yoshinori , Artemov Dmitri 
Published: February 2009

AbstractTo monitor the release of cargo molecules from nanocarriers, a novel MRI/MRS technique was developed and tested. This novel approach uses a simultaneous encapsulation of superparamagnetic iron oxide (SPIO) nanoparticles and either a gadolinium (Gd)‐based paramagnetic contrast agent, Gd‐diethylenetriamine pentaacetic acid bismethylamide(GdDTPA‐BMA), for MRI, or an anticancer agent, 5‐fluorouracil (5‐FU), for MRS. These agents have significantly different diffusion properties due to their different molecular sizes. Strong negative signal enhancement due to the T2 effects of SPIO dominates the positive T1 contrast generated by GdDTPA‐BMA when SPIO and GdDTPA‐BMA are in close proximity (intact form). Positive T1 contrast becomes evident upon release of GdDTPA‐BMA from the carrier once the distance between GdDTPA‐BMA and SPIO molecules is beyond the T2 enhancement range. Similarly, intact nanocarriers loaded with 5‐FU and SPIO have a broad 19F resonance line because line‐width is inversely proportional to T*2, while free 5‐FU appears as a narrow resonance line once it is released from the liposomes. This technique allowed monitoring of the release of cargo molecules from liposomes encapsulating both SPIO and either GdDTPA‐BMA or 5‐FU by MRI/MRS in vitro using 2% agarose gel phantoms. Experimental results demonstrate successful demarcation of the released cargo molecules vs. encapsulated molecules. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Evaluation of the dose distribution gradient in the close vicinity of brachytherapy seeds using electron paramagnetic resonance imaging
Authors: Vanea Emilia S. , Levêque Philippe , Abboud Fadi , Bol Anne , Denis Jean Marc , Kolbun Natallia , Vynckier Stefaan , Gallez Bernard 
Published: February 2009

AbstractElectron paramagnetic resonance (EPR) spectroscopy has been successfully employed to determine radiation dose using alanine. The EPR signal intensity reflects the number of stable free radicals produced, and provides a quantitative measurement of the absorbed dose. The aim of the present study was to explore whether this principle can be extended to provide information on spatial dose distribution using EPR imaging (EPRI). Lithium formate was selected because irradiation induces a single EPR line, a characteristic that is particularly convenient for imaging purposes.125I‐brachytherapy seeds were inserted in tablets made of lithium formate. Images were acquired at 1.1 GHz. Monte Carlo (MC) calculations were used for comparison. The dose gradient can be determined using two‐dimensional (2D) EPR images. Quantitative data correlated with the dose estimated by the MC simulations, although differences were observed. This study provides a first proof‐of‐concept that EPRI can be used to estimate the gradient dose distribution in phantoms after irradiation. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Noise figure limits for circular loop MR coils
Authors: Kumar Ananda , Edelstein William A. , Bottomley Paul A. 
Published: February 2009

AbstractCircular loops are the most common MR detectors. Loop arrays offer improved signal‐to‐noise ratios (SNRs) and spatial resolution, and enable parallel imaging. As loop size decreases, loop noise increases relative to sample noise, ultimately dominating the SNR. Here, relative noise contributions from the sample and the coil are quantified by a coil noise figure (NF), NFcoil, which adds to the conventional system NF. NFcoil is determined from the ratio of unloaded‐to‐loaded coil quality factors Q. Losses from conductors, capacitors, solder joints, eddy currents in overlapped array coils, and the sample are measured and/or computed from 40 to 400 MHz using analytical and full‐wave numerical electromagnetic analysis. The Qs are measured for round wire and tape loops tuned from 50 to 400 MHz. NFcoil is determined as a function of the radius, frequency, and number of tuning capacitors. The computed and experimental Qs and NFcoils agree within ∼10%. The NFcoil values for 3 cm‐diameter wire coils are 3 dB, 1.9 dB, 0.8 dB, 0.2 dB, and 0.1 dB, at 1T, 1.5T, 3T, 7T, and 9.4T, respectively. Wire and tape perform similarly, but tape coils in arrays have substantial eddy current losses. The ability to characterize and reliably predict component‐ and geometry‐associated coil losses is key to designing SNR‐optimized loop and phased‐array detectors. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Counteracting radio frequency inhomogeneity in the human brain at 7 Tesla using strongly modulating pulses
Authors: Boulant N. , Mangin J.‐F. , Amadon A. 
Published: February 2009

AbstractWe report flip angle and spoiled gradient echo measurements at 7 Tesla on human brains in three‐dimensional imaging, using strongly modulating pulses to counteract the transmitted radiofrequency inhomogeneity problem. Compared with the standard square pulse results, three points of improvement are demonstrated, namely: (i) the removal of the bright center (typical at high fields when using a quadrature head coil), (ii) the substantial gain of signal in the regions of lowB1intensity, and (iii) an increased 35% signal uniformity over the whole brain at the flip angle where maximum contrast between white and gray matter occurs. We also find by means of simulations that standard BIR‐4 adiabatic pulses need several times more energy to reach a similar performance at the same field strength. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Comparison of model‐based arterial input functions for dynamic contrast‐enhanced MRI in tumor bearing rats
Authors: McGrath Deirdre M. , Bradley Daniel P. , Tessier Jean L. , Lacey Tony , Taylor Chris J. , Parker Geoffrey J.M. 
Published: February 2009

AbstractWhen using tracer kinetic modeling to analyze dynamic contrast‐enhanced MRI (DCE‐MRI) it is necessary to identify an appropriate arterial input function (AIF). The measured AIF is often poorly sampled in both clinical and preclinical MR systems due to the initial rapid increase in contrast agent concentration and the subsequent large‐scale signal change that occurs in the arteries. However, little work has been carried out to quantify the sensitivity of tracer kinetic modeling parameters to the form of AIF. Using a preclinical experimental data set, we sought to measure the effect of varying model forms of AIF on the extended Kety compartmental model parameters (Ktrans, ve, and vp) through comparison with the results of experimentally acquired high temporal resolution AIFs. The AIF models examined have the potential to be parameterized on lower temporal resolution data to predict the form of the true, higher temporal resolution AIF. The models were also evaluated through application to the population average AIF. It was concluded that, in the instance of low temporal resolution or noisy data, it may be preferable to use a bi‐exponential model applied to the raw data AIF, or when individual measurements are not available a bi‐exponential model of the average AIF. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
About “axial” and “radial” diffusivities
Authors: Wheeler‐Kingshott Claudia A.M. , Cercignani Mara 
Published: February 2009

AbstractThis article presents the potential problems arising from the use of “axial” and “radial” diffusivities, derived from the eigenvalues of the diffusion tensor, and their interpretation in terms of the underlying biophysical properties, such as myelin and axonal density. Simulated and in vivo data are shown. The simulations demonstrate that a change in “radial” diffusivity can cause a fictitious change in “axial” diffusivity and vice versa in voxels characterized by crossing fibers. The in vivo data compare the direction of the principle eigenvector in four different subjects, two healthy and two affected by multiple sclerosis, and show that the angle, α, between the principal eigenvectors of corresponding voxels of registered datasets is greater than 45° in areas of low anisotropy, severe pathology, and partial volume. Also, there are areas of white matter pathology where the “radial” diffusivity is 10% greater than that of the corresponding normal tissue and where the direction of the principal eigenvector is altered by more than 45° compared to the healthy case. This should strongly discourage researchers from interpreting changes of the “axial” and “radial” diffusivities on the basis of the underlying tissue structure, unless accompanied by a thorough investigation of their mathematical and geometrical properties in each dataset studied. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Absolute quantification of cerebral blood flow in neurologically normal volunteers: Dynamic‐susceptibility contrast MRI‐perfusion compared with computed tomography (CT)‐perfusion
Authors: Ziegelitz Doerthe , Starck Göran , Mikkelsen Irene K. , Tullberg Mats , Edsbagge Mikael , Wikkelsö Carsten , Forssell‐Aronson Eva , Holtås Stig , Knutsson Linda 
Published: February 2009

AbstractTo improve the reproducibility of arterial input function (AIF) registration and absolute cerebral blood flow (CBF) quantification in dynamic‐susceptibility MRI‐perfusion (MRP) at 1.5T, we rescaled the AIF by use of a venous output function (VOF). We compared CBF estimates of 20 healthy, elderly volunteers, obtained by computed tomography (CT)‐perfusion (CTP) and MRP on two consecutive days. MRP, calculated without the AIF correction, did not result in any significant correlation with CTP. The rescaled MRP showed fair to moderate correlation with CTP for the central gray matter (GM) and the whole brain. Our results indicate that the method used for correction of partial volume effects (PVEs) improves MRP experiments by reducing AIF‐introduced variance at 1.5T. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Characterization of white matter fiber bundles with T relaxometry and diffusion tensor imaging
Authors: Cherubini Andrea , Péran Patrice , Hagberg Gisela Elisabeth , Varsi Ambra Erika , Luccichenti Giacomo , Caltagirone Carlo , Sabatini Umberto , Spalletta Gianfranco 
Published: February 2009

AbstractIn this study, diffusion tensor imaging (DTI) and T multiecho relaxometry were combined in 30 healthy subjects at 3T, with the aim of characterizing the spatial distribution of relaxation rates in white matter (WM). Region of interest (ROI) analysis was performed in 23 different fiber tracts automatically defined in standard space. Spearman rank analysis was performed on regional values of T, fractional anisotropy (FA), and radial diffusivity (RD). A strong relationship was observed between the location and direction of fiber bundles and relaxation rates, and adjacent fiber bundles with similar orientation showed very different relaxation rates. Moreover, while relaxation rates varied largely between different fiber tracts, variation of the same parameter within the same anatomical fiber bundle across individuals was remarkably limited. The rich variability of relaxation rates in WM and their complex relationship with DTI data suggested that the two techniques might be sensitive to complementary characteristics of myelin structure. This has tremendous potential to allow for a more detailed understanding of brain development and pathology, in particular in the context of age‐related cognitive decline. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Estimating cerebral blood volume with expanded vascular space occupancy slice coverage
Authors: Glielmi Christopher B. , Schuchard Ronald A. , Hu X.P. 
Published: February 2009

AbstractA model for quantifying cerebral blood volume (CBV) based on the vascular space occupancy (VASO) technique and varying the extent of blood nulling yielding task‐related signal changes with various amounts of blood oxygenation level‐dependent (BOLD) and VASO weightings was previously described. Challenges associated with VASO include limited slice coverage and the confounding inflow of fresh blood. In this work, an approach that extends the previous model to multiple slices and accounts for the inflow effect is described and applied to data from a multiecho sequence simultaneously acquiring VASO, cerebral blood flow (CBF), and BOLD images. This method led to CBV values (7.9 ± 0.3 and 5.6 ± 0.3 ml blood/100 ml brain during activation [CBVACT] and rest [CBVREST], respectively) consistent with previous studies using similar visual stimuli. Furthermore, an increase in effective blood relaxation (0.65 ± 0.01) compared to the published value (0.62) was detected, likely reflecting inflow of fresh blood. Finally, cerebral metabolic rate of oxygen (CMRO2) estimates using a multiple compartment model without assumption of CBVREST led to estimates (18.7 ± 17.0%) that were within published ranges. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Anti‐vibration and vibration isolator performance of poly(styrene‐butadiene‐ styrene)/ester‐type polyurethane thermoplastic elastomers
Authors: Wu Jyh‐Horng , Li Chia‐Hao , Chiu Hsien‐Tang , Shong Zhi‐Jian , Tsai Peir‐An 
Published: February 2009

AbstractThis investigation presents novel thermoplastic elastomers (TPEs) based on poly(styrene‐butadiene‐styrene) (SBS) and ester‐type polyurethane (TPU‐EX) materials were prepared with varying compositions. A series of investigations were conducted on the relationships between mechanical properties, dynamic mechanical properties, anti‐vibration and vibration isolator properties given, and the different compositions. The experimental results show incompatibilities between SBS and TPU‐EX. SBS mechanical properties, dynamic mechanical properties, anti‐vibration and vibration isolator properties are improved with an increase in the amount of TPU‐EX, suggesting that the blending of SBS with TPU‐EX was consistent with the compound rule. Based on the obtained results, the viscoelasticity of SBS materials, their capacity to isolate vibration, and their anti‐vibration performance can be adjusted by controlling the proportion of TPU‐EX. Copyright © 2009 John Wiley & Sons, Ltd.
Mammosphere‐derived gene set predicts outcome in patients with ER‐positive breast cancer
Authors: Kok Marleen , Koornstra Rutger H , Margarido Tania C , Fles Renske , Armstrong Nicola J , Linn Sabine C , Van‘t Veer Laura J , Weigelt Britta 
Published: February 2009

AbstractTumourigenic subpopulations with stem cell‐like features have been identified in breast tumours and breast cancer cell lines. The hormone receptor status, molecular characteristics and clinical significance of these cells are still matters of debate. Enrichment for tumourigenic cells without the requirement of surface markers can be achieved by the in vitro mammosphere culture assay. Here we compared the hormone receptor status and genome‐wide gene expression profiles of mammospheres derived from four oestrogen‐receptor (ER) positive breast cancer cell lines with those of the respective parental cells. Immunohistochemistry and gene expression profiling revealed a significant reduction in the expression of progesterone receptor, proliferation and cell cycle regulated genes in mammospheres when compared to parental cell lines. The 200 most differentially expressed genes between mammospheres and parental cell lines were used to generate a ‘mammosphere‐derived’ gene set. Hierarchical clustering of gene expression profiles of two independent cohorts of primary ER‐positive cancers based on the ‘mammosphere‐derived’ gene set revealed that the subgroup of breast cancers with profiles similar to those of mammospheres has a significantly longer overall survival. In conclusion, tumour‐initiating breast cancer cells grown in mammospheres seem to reside in a quiescent state. ER‐positive breast cancers with expression profiles similar to those of mammospheres have a better outcome, providing evidence in support of the concept that outcome of patients with ER‐positive disease is for a large part determined by cell cycle and proliferation activity. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Global proteomic pattern of Tropheryma whipplei: A Whipple's disease bacterium
Authors: Kowalczewska Malgorzata , Villard Claude , Lafitte Daniel , Fenollar Florence , Raoult Didier 
Published: February 2009

AbstractThe proteome of Tropheryma whipplei, the intracellular bacterium responsible for Whipple's disease (WD), was analyzed using two complementary approaches: 2‐DE coupled with MALDI‐TOF and SDS‐PAGE with nanoLC‐MS/MS. This strategy led to the identification of 206 proteins of 808 predicted ORFs, resolving some questions raised by the genomic sequence of this bacterium. We successfully identified antibiotic targets and proteins with predicted N‐terminal signal sequences. Additionally, we identified a family of surface proteins (known as T. whipplei surface proteins (WiSPs)), which are encoded by a unique group of species‐specific genes and serve as both coding regions and DNA repeats that promote genomic recombination. Comparison of the protein expression profiles of the intracellular facultative host‐associated WD bacterium with other host‐associated, intracellular obligate, and environmental bacteria revealed that T. whipplei shares a proteomic expression profile with other host‐associated facultative intracellular bacteria. In summary, this study describes the global protein expression pattern of T. whipplei and reveals some specific features of the T. whipplei proteome.
Exploring membrane and cytoplasm proteomic responses of Alkalimonas amylolytica N10 to different external pHs with combination strategy of de novo peptide sequencing
Authors: Wang Quanhui , Han Huiming , Xue Yanfen , Qian Zhong , Meng Bo , Peng Fuli , Wang Zhuowei , Tong Wei , Zhou Chuanqi , Wang Qian , Guo Yonghao , Li Gang , Liu Siqi , Ma Yanhe 
Published: February 2009

AbstractIdentification of differentially proteomic responses to external pHs would pave an access for understanding of survival mechanisms of bacteria living at extreme pH environment. We cultured Alkalimonas amylolytica N10 (N10), a novel alkaliphilic bacterium found in Lake Chahannor, in media with three different pHs and extracted the correspondent membrane and cytoplasm proteins for proteomic analysis through 2‐DE. The differential 2‐DE spots corresponding to the altered pHs were delivered to MALDI TOF/TOF MS for protein identification. Since the genomic data of strain N10 was unavailable, we encountered a problem at low rate of protein identification with 18.1%. We employed, therefore, a combined strategy of de novo sequencing to analyze MS/MS signals generated from MALDI TOF/TOF MS. A significantly improved rate of protein identification was thus achieved at over than 70.0%. Furthermore, we extensively investigated the expression of these pH‐dependent N10 genes using Western blot and real‐time PCR. The conclusions drawn from immunoblot and mRNA measurements were mostly in agreement with the proteomic observations. We conducted the bioinformatic analysis to all the pH‐dependent N10 proteins and found that some membrane proteins participated in iron transport were differentially expressed as external pH elevated and most of differential proteins with increased or bell‐shape mode of pH‐dependence were involved in bioenergetic process and metabolism of carbohydrates, fatty acid, amino acids, and nucleotides. Our data thus provide a functional profile of the pH‐responsive proteins in alkaliphiles, leading to elucidation of alkaliphilic‐adaptive mechanism.
Phosphoproteomic analysis of ethylene‐regulated protein phosphorylation in etiolated seedlings of Arabidopsis mutant ein2 using two‐dimensional separations coupled with a hybrid quadrupole time‐of‐flight mass spectrometer
Authors: Li Hao , Wong Wai Shing , Zhu Lin , Guo Hong Wei , Ecker Joseph , Li Ning 
Published: February 2009

AbstractEthylene regulates a variety of stress responses and developmental adaptation in plants. In the present study, the phosphoproteomics is adopted to investigate the differential protein phosphorylation by ethylene in Arabidopsis ethylene‐insensitive 2 (ein2) mutant. A total of 224 phosphopeptides were identified, of which 64 phosphopeptides were detected three or more times. Ethylene induces a general reduction in phosphorylated proteins in ein2. Totally, three ethylene‐enhanced and three ethylene‐repressible unique phosphopeptides were identified, respectively. Classification of the cellular functions of these phosphoproteins revealed that 55.5% of them are related to signaling and gene expression. Peptide sequence alignment reveals two highly conserved phosphorylation motifs, PRVD/GSx and SPDYxx. Alignment of these phosphopeptides with Arabidopsis proteins reveals five phosphorylation motifs. Both ethylene‐enhanced and ‐repressible phosphopeptides present in these motifs. EIL‐1, ERF110 transcription factors and Hua enhancer 4 (HEN4) are predicted to contain one of the phosphorylation motifs. The phosphorylation of the motif‐containing peptides has been validated by the in vitro kinase assays coupled with MS analysis. The differential regulation of phosphorylation by ethylene is substantiated by Western dot blot analysis. Taken together, these results suggest that ethylene signals may be transduced by a phosphor‐relay from receptors to transcriptional events via both ein2‐dependent and ‐independent pathways.
Energetic determinants of protein binding specificity: Insights into protein interaction networks
Authors: Carbonell Pablo , Nussinov Ruth , del Sol Antonio 
Published: February 2009

AbstractOne of the challenges of the postgenomic era is to provide a more realistic representation of cellular processes by combining a systems biology description of functional networks with information on their interacting components. Here we carried out a systematic large‐scale computational study on a structural protein–protein interaction network dataset in order to dissect thermodynamic characteristics of binding determining the interplay between protein affinity and specificity. As expected, interactions involving specific binding sites display higher affinities than those of promiscuous binding sites. Next, in order to investigate a possible role of modular distribution of hot spots in binding specificity, we divided binding sites into modules previously shown to be energetically independent. In general, hot spots that interact with different partners are located in different modules. We further observed that common hot spots tend to interact with partners exhibiting common binding motifs, whereas different hot spots tend to interact with partners with different motifs. Thus, energetic properties of binding sites provide insights into the way proteins modulate interactions with different partners. Knowledge of those factors playing a role in protein specificity is important for understanding how proteins acquire additional partners during evolution. It should also be useful in drug design.