bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiple genomic alterations on 21q22 predict various TMPRSS2/ERG fusion transcripts in human prostate cancers
Authors: Liu Wennuan , Ewing Charles M , Chang Bao‐Li , Li Tao , Sun Jishan , Turner Aubrey R. , Dimitrov Latchezar , Zhu Yi , Sun Jielin , Kim Jin Woo , Zheng S. Lilly , Isaacs William B. , Xu Jianfeng
Published: July 2007

A number of TMPRSS2/ERG fusion transcripts have been reported since the discovery that recurrent genomic rearrangements result in the fusion of TMPRSS2 and ETS family member genes. In this article we present evidence demonstrating that multiple genomic alterations contribute to the formation of various TMPRSS2/ERG transcripts. Using allele‐specific analysis of the data generated from the GeneChip 500K SNP array we observed both hemizygous and homozygous deletions occurring at different locations between and within TMPRSS2 and ERG in prostate cancers. The 500K SNP array enabled us to fine map the start and end of each deletion to specific introns of these two genes, and to predict a variety of fusion transcripts, including a new form which was confirmed by sequence analysis of the fusion transcripts in various tumors. We also inferred that translocation is an additional mechanism of fusion for these two genes in some tumors, based on largely diploid genomic DNA between TMPRSS and ERG, and different fusion transcripts produced in these tumors. Using a bioinformatics approach, we then uncovered the consensus sequences in the regions harboring the breakpoints of the deletions. These consensus sequences were homologous to the human Alu‐Sq and Alu‐Sp subfamily consensus sequences, with more than 80% homology. The presence/absence of Alu family consensus sequence in the introns of TMPRSS2 and ERG correlates with the presence/absence of fusion transcripts of theses two genes, indicating that these consensus sequences may contribute to genomic deletions and the fusion of TMPRSS2 and ERG in prostate cancer. © 2007 Wiley‐Liss, Inc.
Frequency and characterization of HMGA2 and HMGA1 rearrangements in mesenchymal tumors of the lower genital tract
Authors: Medeiros Fabiola , Erickson‐Johnson Michele R. , Keeney Gary L. , Clayton Amy C. , Nascimento Antonio G. , Wang Xiaoke , Oliveira Andre M.
Published: July 2007

Mesenchymal tumors of the lower genital tract predominantly occur in women of reproductive age and are mainly represented by aggressive angiomyxoma (AAM) and angiomyofibroblastoma (AMF). Whether these tumors are different phenotypic expressions of the same biological entity is still debatable. Genetic rearrangements of HMGA2 have been reported in a few cases of AAM but its frequency and clinicobiological implications have not been studied systematically. We evaluated 90 cases of mesenchymal tumors of the lower genital tract that comprised 42 AAMs, 18 AMFs, 6 cellular angiofibromas, 5 fibroepithelial stromal polyps, 15 genital leiomyomas, 3 superficial angiomyxomas, and 1 spindle cell lipoma. Fluorescence in situ hybridization was used to identify rearrangements of HMGA2 and its homologue HMGA1. HMGA2 rearrangements were identified in 14 AAMs (33%) and in 1 vaginal leiomyoma. All other tumors were negative for HMGA2 rearrangements. HMGA1 rearrangement was not found in any of the cases. RT‐PCR confirmed transcriptional upregulation of HMGA2 only in tumors with HMGA2 rearrangements. Standard cytogenetic analyses were performed in two AAMs and one AMF. One AAM had a t(1;12)(p32;q15); the other tumors had normal karyotypes. Mapping and sequence analysis of the breakpoint showed fusion to the 3′ untranslated region of HMGA2 to genomic sequences derived from the contig NT 032977.8 on chromosome 1p32. Our findings support the hypothesis that AAM and AMF are distinct biological entities. The diagnostic usefulness of HMGA2 rearrangements to differentiate between AAM and other tumors of the lower genital tract may be limited due to the their low frequency. © 2007 Wiley‐Liss, Inc.
Hierarchical Bayes prioritization of marker associations from a genome‐wide association scan for further investigation
Authors: Lewinger Juan Pablo , Conti David V. , Baurley James W. , Triche Timothy J. , Thomas Duncan C.
Published: July 2007

We describe a hierarchical regression modeling approach to selection of a subset of markers from the first stage of a genomewide association scan to carry forward to subsequent stages for testing on an independent set of subjects. Rather than simply selecting a subset of most significant marker‐disease associations at some cutoff chosen to maximize the cost efficiency of a multistage design, we propose a prior model for the true noncentrality parameters of these associations composed of a large mass at zero and a continuous distribution of nonzero values. The prior probability of nonzero values and their prior means can be functions of various covariates characterizing each marker, such as their location relative to genes or evolutionary conserved regions, or prior linkage or association data. We propose to take the top ranked posterior expectations of the noncentrality parameters for confirmation in later stages of a genomewide scan. The statistical performance of this approach is compared with the traditional p‐value ranking by simulation studies. We show that the ranking by posterior expectations performs better at selecting the true positive association than a simple ranking of p‐values if at least some of the prior covariates have predictive value. Genet. Epidemiol. 31, 2007. © 2007 Wiley‐Liss, Inc.
MAC1 mediates LPS‐induced production of superoxide by microglia: The role of pattern recognition receptors in dopaminergic neurotoxicity
Authors: Pei Zhong , Pang Hao , Qian Li , Yang Sufen , Wang Tonggauang , Zhang Wei , Wu Xeufei , Dallas Shannon , Wilson Belinda , Reece Jeffrey M. , Miller David S. , Hong Jau‐Shyong , Block Michelle L.
Published: July 2007

Microglia‐derived superoxide is critical for the inflammation‐induced selective loss of dopaminergic (DA) neurons, but the underlying mechanisms of microglial activation remain poorly defined. Using neuron‐glia and microglia‐enriched cultures from mice deficient in the MAC1 receptor (MAC1−/−), we demonstrate that lipopolysaccharide (LPS) treatment results in lower TNFα response, attenuated loss of DA neurons, and absence of extracellular superoxide production in MAC1−/−cultures. Microglia accumulated fluorescently labeled LPS in punctate compartments associated with the plasma membrane, intracellular vesicles, and the Golgi apparatus. Cytochalasin D (CD), an inhibitor of phagocytosis, blocked LPS internalization. However, microglia derived from Toll‐like receptor 4 deficient mice and MAC1−/−mice failed to show a significant decrease in intracellular accumulation of labeled LPS, when compared with controls. Pretreatment with the scavenger receptor inhibitor, fucoidan, inhibited 79% of LPS accumulation in microglia without affecting superoxide, indicating that LPS internalization and superoxide production are mediated by separate phagocytosis receptors. Together, these data demonstrate that MAC1 is essential for LPS‐induced superoxide from microglia, implicating MAC1 as a critical trigger of microglial‐derived oxidative stress during inflammation‐mediated neurodegeneration. © 2007 Wiley‐Liss, Inc.
Dispensability and dynamics of caveolin-1 during liver regeneration and in isolated hepatic cells
Authors: Mayoral Rafael , Fernández-Martínez Amalia , Roy Rosa , Boscá Lisardo , Martín-Sanz Paloma
Published: July 2007

Caveolae participate in several cellular processes such as vesicular transport, cholesterol homeostasis, regulation of signal transduction, integrin signaling, and cell growth. The expression and functional role of caveolin (Cav), the most abundant protein of caveolae, has been reported in liver and in different hepatocyte cell lines, in human cirrhotic liver, and in hepatocellular carcinomas. The role of Cav-1 in liver regeneration after partial hepatectomy (PH) has been investigated as a model of liver proliferation

in vivo

. Our results show that Cav-1 increases in liver after PH with a redistribution of the protein from the caveola-enriched domain to the noncaveolar fraction. Moreover, the Cav-1 located in the noncaveolar fraction is phosphorylated in tyrosine 14, even though the Cav-1 gene is dispensable for liver regeneration after PH, as deduced from data obtained with commercially available animals lacking this gene. In addition to this, the proinflammatory stimulation of hepatocytes induces Cav-1 translocation to a noncaveolar fraction and tyrosine 14 phosphorylation mainly through the activation of tyrosine kinases such as Src.

Conclusion:

These results support a dynamic role for Cav-1 in liver proliferation both

in vivo

after PH and

in vitro

in cultured hepatic cell lines, but with minimal implications for the liver regeneration process. (Hepatology 2007.)
Differences between Caucasian, African American, and Hispanic patients with primary biliary cirrhosis in the United States
Authors: Peters Marion G. , Di Bisceglie Adrian M. , Kowdley Kris V. , Flye Nancy L. , Luketic Velimir A. , Munoz Santiago J. , Garcia-Tsao Guadalupe , Boyer Thomas D. , Lake John R. , Bonacini Maurizio , Combes Burton
Published: July 2007

Primary biliary cirrhosis (PBC) is an uncommon chronic cholestatic liver disease that primarily afflicts young and middle-aged Caucasian women; there are limited data on the clinical presentation and disease severity among non-Caucasian patients with this disease. The goal of this study was to examine differences in the severity of liver disease between Caucasian and non-Caucasian patients with PBC screened for enrollment in a large national multicenter clinical trial. Demographic features, symptoms, physical findings, and laboratory tests obtained during screening were examined in 535 patients with PBC with respect to ethnicity, gender, and antimitochondrial antibody (AMA) status; 73 of 535 (13.6%) were non-Caucasian (21 were African American, and 42 were Hispanic). Non-Caucasians were more likely than Caucasians to be ineligible for participation in the clinical trial (46.5% versus 25.1%,

P

= 0.0001), primarily because of greater disease severity. African Americans and Hispanics were also more likely to have a lower activity level, more severe pruritus, and more advanced disease. However, the mean age, male-to-female ratio, and seroprevalence of AMA positivity were similar between the 2 groups.

Conclusion:

Liver disease severity at clinical presentation is higher among non-Caucasians than Caucasians with PBC, and this cannot be explained by demographic or serologic features alone. Possible mechanisms underlying this health discrepancy are not clear, but increased awareness of PBC as a cause of chronic cholestatic liver disease is critical in evaluating non-Caucasian patients in the United States. (Hepatology 2007.)
Efficacy of a novel histone deacetylase inhibitor in murine models of hepatocellular carcinoma
Authors: Lu Yen-Shen , Kashida Yoko , Kulp Samuel K. , Wang Yu-Chieh , Wang Dasheng , Hung Jui-Hsiang , Tang Monica , Lin Zhong-Zhe , Chen Te-Jung , Cheng Ann-Lii , Chen Ching-Shih
Published: July 2007

Hepatocellular carcinoma (HCC) is a leading cause of cancer death worldwide, yet effective therapeutic options for advanced HCC are limited. This study was aimed at assessing the antitumor effect of a novel phenylbutyrate-derived histone deacetylase (HDAC) inhibitor, OSU-HDAC42, vis-à-vis suberoylanilide hydroxamic acid (SAHA), in

in vitro

and

in vivo

models of human HCC. OSU-HDAC42 was several times more potent than SAHA in suppressing the viability of PLC5, Huh7, and Hep3B cells with submicromolar median inhibitory concentration (IC50) values. With respect to SAHA, OSU-HDAC42 exhibited greater apoptogenic potency, which was associated with reduced levels of the apoptotic regulators phosphorylated Akt B-cell lymphoma-xL, survivin, cellular inhibitor of apoptosis protein 1, and cellular inhibitor of apoptosis protein 2. The

in vivo

efficacy of OSU-HDAC42 versus SAHA was assessed in orthotopic and subcutaneous xenograft tumor models in athymic nude mice. Daily oral treatments with OSU-HDAC42 and SAHA, both at 25 mg/kg, suppressed the growth of orthotopic PLC5 tumor xenografts by 91% and 66%, respectively, and of established subcutaneous PLC5 tumor xenografts by 85% and 56%, respectively. This differential tumor suppression correlated with the modulation of intratumoral biomarkers associated with HDAC inhibition and apoptosis regulation. Moreover, the oral administration of OSU-HDAC42 at 50 mg/kg every other day markedly suppressed ectopic tumor growth in mice bearing large tumor burdens (500 mm3) at the start of treatment.

Conclusion:

OSU-HDAC42 is a potent, orally bioavailable inhibitor of HDAC with a broad spectrum of antitumor activity that includes targets regulating multiple aspects of cancer cell survival. These results suggest that OSU-HDAC42 has clinical value in therapeutic strategies for HCC. (HEPATOLOGY 2007.)
Liposome‐encapsulated doxorubicin in combination with cyclophosphamide, vincristine, prednisone and rituximab in patients with lymphoma and concurrent cardiac diseases or pre‐treated with anthracyclines
Authors: Rigacci Luigi , Mappa Silvia , Nassi Luca , Alterini Renato , Carrai Valentina , Bernardi Franco , Bosi Alberto
Published: July 2007

Background

To assess the efficacy and safety of the combination of non‐pegylated liposome‐encapsulated doxorubicin (Myocet®) with cyclophosphamide, vincristine, prednisone and rituximab (R‐COMP) in patients with aggressive non‐Hodgkin's B‐cell lymphomas.

Methods

Twenty‐one patients were selected for the presence of negative concurrent clinical features such as cardiac comorbidity and/or previous treatment with anthracycline‐based regimens. Liposome‐encapsulated doxorubicin at a dose of 50 mg/m2 was administered in association with cyclophosphamide (750 mg/m2), vincristine (1.4 mg/m2), prednisone (40 mg/m2) and rituximab (375 mg/m2) every 21 days for four to six cycles unless progression or unacceptable toxicity occurred.

Results

A complete response (CR) was obtained in 16/21 patients (76%), three patients achieved a partial response (14%), with an overall response rate of 90%. Two patients (10%) did not respond to therapy. After a median follow‐up of 13 months (range 2–36 months), 2/16 CR patients relapsed, with a disease‐free survival (DFS) of 78%.

Conclusions

The replacement of doxorubicin with its non‐pegylated liposomal pharmaceutical analogue was well tolerated and highly effective in inducing remission in this group of patients at high risk for cardiac toxicity or previously treated with anthracyclines. Its high tolerability and low incidence of cardiac events (only one patient) warrants further studies to confirm the clinical benefits of liposomal doxorubicin in this subset of patients. Copyright © 2007 John Wiley & Sons, Ltd.
WebProp: Web interface forab initiocalculation of molecular one‐electron properties
Authors: Ganesh V. , Kavathekar Ritwik , Rahalkar Anuja , Gadre Shridhar R.
Published: July 2007

This note describes the features and implementation issues of WebProp, a web‐based interface for evaluatingab initioquality one‐electron properties. The interface code is written in HTML and Python, while the backend is handled using Python and our indigenously developed code INDPROP for property evaluation. A novel feature of this setup is that it provides a simple interface for computing first principle one‐electron properties of small to medium sized molecules. To facilitate computation of otherwise expensive calculations on large molecular systems, we employ the Molecular Tailoring Approach (MTA) developed in our laboratory to obtain the density matrix (DM). This DM is then employed for computing the one‐electron properties of these systems. The backend transparently handles jobs submitted by the user and runs them either on a single machine or over a grid of compute nodes. The results of the calculations, which include the summary and the files necessary for visualization of one‐electron properties, are e‐mailed to the user. The user can either directly use the data or visualize it using visualization tools such as UNIVIS‐2000 or Drishti. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Acute intermittent porphyria: vector optimization for gene therapy
Authors: Yasuda Makiko , Domaradzki Maciej E. , Armentano Donna , Cheng Seng H. , Bishop David F. , Desnick Robert J.
Published: July 2007

Background

Acute intermittent porphyria (AIP) is an autosomal dominant disorder caused by the half‐normal activity of hydroxymethylbilane synthase (HMB‐synthase). Affected individuals can experience episodic, life‐threatening, acute neurological attacks that are precipitated by various drugs, dieting, and hormonal changes. Intravenous hematin is used to treat the attacks, but a more effective, preventive therapy is needed, especially for patients with frequent attacks. Since the disease is a hepatic encephalopathy, efforts were focused towards evaluating four different combinations of liver‐specific enhancers and promoters for maximal hepatic HMB‐synthase expression.

Methods

Four different mammalian expression vectors, each carrying a unique combination of liver‐specific enhancers and promoters driving murine HMB‐synthase cDNA expression, were transiently transfected into HepG2 cells. The vectors included: HMBS‐1; human α1‐microglobulin enhancer/α1‐antityrpsin promoter (α1Me/α1ATp), HMBS‐2; α1Me/human serum albumin promoter (α1Me/SAp), HMBS‐3; human prothrombin enhancer/SAp (PTe/SAp), and HMBS‐4; (PTe/α1ATp). Each HMB‐synthase construct and a luciferase reporter construct were hydrodynamically coinjected into mice with HMB‐synthase deficiency and evaluated for hepatic expression 24 h post‐injection, the time‐point of peak hepatic HMB‐synthase expression.

Results

Following transient transfection into HepG2 cells, HMBS‐1 (α1Me/α1ATp) had the highest HMB‐synthase expression level, with an ∼8‐fold increase over endogenous cellular activities. Construct HMBS‐1 also had the highest hepatic HMB‐synthase activity following hydrodynamic delivery into HMB‐synthase deficient mice, with a ∼6‐fold increase over saline‐treated mice.

Conclusions

These studies support the use of a gene therapy vector containing the α1Me/α1ATp combination for preclinical studies of the efficacy and safety of liver‐targeted gene therapy for AIP. Copyright © 2007 John Wiley & Sons, Ltd.
Can homogeneous preparation encoding (HoPE) help reduce scan time in abdominal MRI? A clinical evaluation
Authors: Paul Dominik , Frydrychowicz Alex , Walcher Jens , Fautz Hans‐Peter , Hennig Jürgen , Langer Matthias , Schäfer Oliver
Published: July 2007

Purpose

To evaluate time efficiency, image quality, and diagnostic value of a clinical routine homogeneous preparation encoding (HoPE) imaging protocol in different malign and inflammatory abdominal conditions.

Materials and Methods

A total of 14 healthy volunteers and 40 patients were examined after written informed consent and approval of the local ethics committee. A standard abdominal T1‐weighted (T1W) fat‐saturated gradient‐echo protocol was compared to the HoPE sequence protocol ensuring for comparable imaging parameters. Examinations were performed on a 1.5‐T Siemens Avanto equipped with a multichannel body‐array coil. Image analysis was performed with respect to contrast‐to‐noise ratio (CNR) and signal‐to‐noise ratio (SNR), level of fat suppression (FS), generation of artifacts, and overall image quality by two blinded radiologists.

Results

In addition to comparable results in overall image quality and FS level, the HoPE sequence protocol provided a reduction in acquisition time of up to 40%. In addition, artifact generation was same or even reduced with respect to pulsation. Quantitative SNR analysis showed strong correlation between HoPE and the conventional method.

Conclusion

The HoPE technique is a feasible and time‐saving alternative for clinical abdominal MRI. Future studies will have to be conducted on larger patient collectives to strengthen the impact of this promising technique for FS imaging and to prove its accuracy. J. Magn. Reson. Imaging 2007;26:442–447. © 2007 Wiley‐Liss, Inc.
Cardiac MRI in mice at 9.4 Tesla with a transmit‐receive surface coil and a cardiac‐tailored intensity‐correction algorithm
Authors: Sosnovik David E. , Dai Guangping , Nahrendorf Matthias , Rosen Bruce R. , Seethamraju Ravi
Published: July 2007

Purpose

To evaluate the use of a transmit‐receive surface (TRS) coil and a cardiac‐tailored intensity‐correction algorithm for cardiac MRI in mice at 9.4 Tesla (9.4T).

Materials and Methods

Fast low‐angle shot (FLASH) cines, with and without delays alternating with nutations for tailored excitation (DANTE) tagging, were acquired in 13 mice. An intensity‐correction algorithm was developed to compensate for the sensitivity profile of the surface coil, and was tailored to account for the unique distribution of noise and flow artifacts in cardiac MR images.

Results

Image quality was extremely high and allowed fine structures such as trabeculations, valve cusps, and coronary arteries to be clearly visualized. The tag lines created with the surface coil were also sharp and clearly visible. Application of the intensity‐correction algorithm improved signal intensity, tissue contrast, and image quality even further. Importantly, the cardiac‐tailored properties of the correction algorithm prevented noise and flow artifacts from being significantly amplified.

Conclusion

The feasibility and value of cardiac MRI in mice with a TRS coil has been demonstrated. In addition, a cardiac‐tailored intensity‐correction algorithm has been developed and shown to improve image quality even further. The use of these techniques could produce significant potential benefits over a broad range of scanners, coil configurations, and field strengths. J. Magn. Reson. Imaging 2007;26:279–287. © 2007 Wiley‐Liss, Inc.
Detection of cerebral metabolites by single‐voxel‐based PRESS and COSY techniques at 3T
Authors: Velan S. Sendhil , Lemieux Susan K. , Raylman Raymond R. , Boling Warren , Hobbs Gerald R. , Spencer Richard G. , Sridhar Rajagopalan , Kuppusamy Periannan , Thomas M. Albert
Published: July 2007

Purpose

To compare point‐resolved spectroscopy (PRESS) and localized two‐dimensional (2D) correlated spectroscopy (L‐COSY) in the detection of cerebral metabolites in humans on a clinical scanner at 3T and to estimate their respective inter‐ and intrasubject variances.

Materials and Methods

Measurements were made on nine healthy subjects to assess intersubject variance, and daily on a single subject over a period of seven days to assess intrasubject variance. All L‐COSY measurements were performed with a voxel size of 27 mL (3 × 3 × 3 cm3) and a measurement time of ∼34 minutes in the occipitoparietal lobe of the brain. Relative metabolite concentrations were estimated with respect to N‐methyl creatine.

Results

While the sensitivity of PRESS is twice that of L‐COSY, the greater spectral resolution offered by L‐COSY resulted in greater consistency in estimates of the concentrations of several cerebral metabolites, as indicated by a superior intraclass correlation and a significantly lower standard deviation (SD) in a matched pair intrasubject analysis.

Conclusion

Our pilot results demonstrate that L‐COSY is an effective approach for resolving cerebral metabolites, and demonstrates a lower coefficient of variance (CV) than the conventional 1D localized spectroscopic approach using LC Model for quantification. J. Magn. Reson. Imaging 2007;26:405–409. © 2007 Wiley‐Liss, Inc.
Regional pulmonary perfusion using model‐free analysis of contrast‐enhanced MRI in meconium‐aspirated piglets
Authors: Ryhammer Pia , Pedersen Michael , Ringgaard Steffen , Ravn Hanne
Published: July 2007

Purpose

To investigate if dynamic contrast‐enhanced MRI in lungs could add new information to pulmonary hypertension in a newborn piglet model.

Materials and Methods

Six newborn piglets were subjected to instillation of meconium following treatment with sildenafil. Before and after both of these events, dynamic contrast‐enhanced MRI was performed to determine pulmonary blood flow (PBF) using a model‐free deconvolution of the dynamic signal‐time curve, together with invasive measurements of mean airway pressure (PAW), cardiac output (CO), and oxygenation index (OI).

Results

Meconium instillation caused a significant increase in PAW (P < 0.05) accompanied by a marked increase in OI, the average PBF in the four lung regions (apical‐anterior, apical‐posterior, distal‐anterior, and distal‐posterior) decreased significantly by 33% (P < 0.001), but it did not significantly affect CO. On the other hand, infusion of sildenafil caused a significant increase in CO (P < 0.01), and administration resulted mainly in an increased PBF in the distal parts of the lungs.

Conclusion

By using dynamic contrast‐enhanced MRI, we demonstrated a marked decrease in PBF following instillation of meconium, which was not followed by an equivalent decrease in CO, suggesting that measurements of CO inadequately reflect the intrapulmonary changes in the blood circulation. J. Magn. Reson. Imaging 2007;26:296–303. © 2007 Wiley‐Liss, Inc.
Implementation and validation of localized constant‐time correlated spectroscopy (LCT‐COSY) on a clinical 3T MRI scanner for investigation of muscle metabolism
Authors: Velan S. Sendhil , Ramamurthy Senthil , Ainala Srilatha , Durst Christopher , Lemieux Susan K. , Raylman Raymond R. , Spencer Richard G. , Thomas M. Albert
Published: July 2007

Purpose

To implement and evaluate a novel single‐volume two‐dimensional localized constant‐time‐based correlated spectroscopy (2D LCT‐COSY) sequence on a clinical 3T MR scanner. This sequence exhibits homonuclear decoupling along the F1 dimension, leading to improved spectral resolution compared to that of non‐constant‐time localized correlated spectroscopy (L–COSY).

Materials and Methods

A GE 3T MR scanner equipped with a quadrature transmit and receive extremity coil was used in this study. The 2D LCT‐COSY sequence was programmed using General Electric's EPIC compiler. Simulations for a two‐spin 1/2 system were performed using GAMMA libraries to evaluate the theoretical performance of the sequences, and were also compared with corresponding phantom experiments using trans‐cinnamic acid. Finally, spectra were acquired from the soleus muscle of healthy volunteers in order to evaluate performance in vivo.

Results

Simulations and experimental results confirmed the improved spectral resolution of LCT‐COSY over L–COSY, as well as its homonuclear decoupling performance. The behavior of resonance amplitudes as a function of evolution time in the experiment also was appropriately reflected by the simulation. Corresponding results were obtained for the in vivo muscle spectra, in which separation of overlapping olefinic and allylic methylene protons from the intra‐ and extramyocellular lipids (IMCL and EMCL, respectively) was achieved.

Conclusion

Simulations and experimental results in vitro and in vivo demonstrate the strengths of LCT‐COSY. This technique can be implemented on systems of any field strength, and has the potential to separate overlapping metabolites in tissue when employed on high‐field clinical MRI scanners equipped for proton spectroscopy. J. Magn. Reson. Imaging 2007;26:410–417. © 2007 Wiley‐Liss, Inc.
Investigation of axonal magnetic fields in the human corpus callosum using visual stimulation based on MR signal modulation
Authors: Chow Li Sze , Cook Greg G. , Whitby Elspeth , Paley Martyn N.J.
Published: July 2007

Purpose

To investigate the possibility of detecting visually‐evoked axonal currents in the splenium of the human corpus callosum using a 3.0T MRI system.

Materials and Methods

Axonal currents produce weak and transient magnetic fields, and the components of these that lie parallel to the B0 field of the MRI system can potentially modulate the MR signal, which can be detected as an integrated effect over time. A fast gradient‐echo echo‐planar imaging (GE‐EPI) sequence with short TR and intermediate TE was employed in an attempt to detect such axonal currents using light‐emitting diode (LED) visual stimulation paradigms.

Results

The mean magnitude signal change, expressed relative to the fully relaxed equilibrium signal calculated from the measured value using the known T1 of white matter, was 0.014 ± 0.004% at TE = 30 msec. This corresponded to a mean axonal field of 0.11 ± 0.03 nT, according to the hypothesis that the axonal currents create a Lorentzian field distribution within an imaging voxel.

Conclusion

Measured frequency spectra and statistical mapping using the general linear model (GLM) showed evidence of the stimulus localized within the splenium of the corpus callosum, which was not thought to be due to motion artifacts or physiological responses. J. Magn. Reson. Imaging 2007;26:265–273. © 2007 Wiley‐Liss, Inc.
Prospective evaluation of nonenhanced MR imaging in acute pancreatitis
Authors: Viremouneix Loic , Monneuse Olivier , Gautier Guillaume , Gruner Laurent , Giorgi Roch , Allaouchiche Bernard , Pilleul Frank
Published: July 2007

Purpose

To compare the value of nonenhanced (NE) magnetic resonance imaging (MRI) (NE‐MRI) with contrast‐enhanced (CE) computed tomography (CT) (CE‐CT) scan in assessing acute pancreatitis (AP) and in evaluating the severity index (SI) with clinical outcome.

Materials and Methods

Patients with AP were prospectively investigated by CE‐CT scan and NE‐MRI on admission. MRI was performed with fat‐saturated T1‐weighted imaging, T2‐weighted imaging, and MR cholangiopancreatography (MRCP). Balthazar's grading system was used to evaluate the NE‐MRI severity index (CTSI, MRISI) and it was compared to the clinical outcome.

Results

A total of 90 patients (median age = 55 years) were included in the study. AP was of biliary etiology in 37 patients (41%). On admission, AP was assessed as grade III by CTSI in four patients (4%), whereas 19 patients were classified grade III by MRISI. The coefficient correlation between CTSI and MRISI was good, with r = 0.6 (P < 0.001). Considering CE‐CT scan as the gold standard, sensitivity (Sn), specificity (Sp), positive predictive value (PPV), and negative predictive value (NPV) of NE‐MRI for detecting severe AP based on imaging criteria were 100%, 82.6%, 100%, and 21%, respectively. NE‐MRI discriminates normal pancreatic parenchyma from edema and necrosis with a correlation between morbidity (P < 0.008).

Conclusion

NE‐MRI seems to be a reliable method of staging AP severity in comparison to CE‐CT scan. J. Magn. Reson. Imaging 2007;26:331–338. © 2007 Wiley‐Liss, Inc.
Preparative isolation and purification of sinomenine from Sinomenium acutum by centrifugal partition chromatography
Authors: Cheong Jong Hye , Kim Chul Young , Kim Jinwoong
Published: July 2007

Preparative centrifugal partition chromatography (CPC) was successfully carried out for the separation of sinomenine from the methanolic extract of Sinomenium acutum stems and rhizomes. The optimum two‐phase solvent system of CPC was composed of n‐hexane/ethyl acetate/methanol/water at a volume ratio of 1:6:2:8 (v/v/v/v) with 0.1% triethylamine (TEA). Preparative CPC yielded 44.3 mg of sinomenine from 400 mg of MeOH extract with a purity of 96.9%.
Chip‐based nano‐LC‐MS/MS identification of proteins in complex biological samples using a novel polymer microfluidic device
Authors: Srbek Jan , Eickhoff Jan , Effelsberg Uwe , Kraiczek Karsten , van de Goor Tom , Coufal Pavel
Published: July 2007

Although the proteome of each organism is unambiguously coded in its genome, the proteome shows the real biology in action in each particular organism. New powerful tools are being developed for biochemists and biologists to analyze complex biological samples for studying the complete protein supplement of the genome,i. e., the proteome. There are several methods available for proteome analysis including 2‐DE and several forms of MS. In recent years, technologies such as microfluidics and array‐based systems have appeared in the field of analysis, identification, and quantification of proteins. These novel approaches might help in solving current technical challenges in proteomics. This paper presents a practical application of the first commercially available microfluidic nano‐ESI device coupled with nano‐LC (i. e., HPLC‐chip) for the analysis of samples of some biological protein mixtures.
A rapid RP‐HPTLC densitometry method for simultaneous determination of major flavonoids in important medicinal plants
Authors: Bhandari Pamita , Kumar Neeraj , Gupta Ajai P. , Singh Bikram , Kaul Vijay K.
Published: July 2007

A simple, sensitive, selective, precise, and robust high‐performance TLC (HPTLC) method was developed and validated for determination of flavonoids in herbal extracts Bauhinia variegata, Bacopa monnieri, Centella asiatica, Ginkgo biloba, Lonicera japonica, Rosa bourboniana, Rosa brunonii, and Rosa damascena. The HPTLC of flavonoids was performed on RP‐18 F254 TLC plates with dual run, water (5% formic acid)/methanol (70:30) and water (5% formic acid)/methanol (50:50) as mobile phases. Densitometric determination of flavonoids was performed at λ = 280 nm in reflectance/absorbance mode. The linear regression analysis data for the calibration plots showed a good linear relationship with r2 = 0.998 ± 0.0003 in the concentration range of 150–800 ng/spot for apigenin and rutin and 200–1000 ng/spot for quercetin, luteolin, and quercitrin with respect to peak area. The average recovery for apigenin, quercetin, rutin, luteolin, and quercitrin was 97–99.8% indicating the excellent reproducibility. Statistical analysis of the data showed that the method is reproducible and selective for determination of flavonoids.
High‐performance thin‐layer chromatographic method for quantitative determination of 4α‐methyl‐24β‐ethyl‐5α‐cholesta‐14,25‐dien‐3β‐ol, 24β‐ethylcholesta‐5,9(11),22E‐trien‐3β‐ol, and betulinic acid in Clerodendrum inerme
Authors: Pandey Richa , Verma Ram K. , Gupta Madan M.
Published: July 2007

A sensitive, selective, precise, and robust high‐performance thin‐layer chromatography method was developed and validated for analysis of two new recently isolated sterols, 4α‐methyl‐24β‐ethyl‐5α‐cholesta‐14,25‐dien‐3β‐ol (1) and 24β‐ethylcholesta‐5,9(11),22E‐trien‐3β‐ol (2), and a triterpene, betulinic acid (3), in Clerodendrum inerme extract. The method employed HPTLC plates precoated with silica gel 60F254 as the stationary phase. To achieve good separation, an optimised mobile phase consisting of toluene‐acetone (94:06, v/v) was used (Rf 0.48, 0.34, and 0.22 for compounds 1, 2, and 3, respectively). Densitometric determination of the above compounds was carried out in reflection/absorption mode at 620 nm. Optimised chromatographic conditions provide well separated compact spots for the compounds 1, 2, and 3. The calibration curves were linear in the concentration range of 100–2500 ng/spot. The method was validated for precision, robustness, and recovery. The limits of detection and quantitation were 5, 6, and 10 μg/mL and 14, 18, and 29 μg/mL, respectively, for 1, 2, and 3. The method reported here is reproducible and convenient for quantitative analysis of these compounds in the aerial parts of C. inerme.
Preparation of single‐walled carbon nanotube fiber coating for solid‐phase microextraction of organochlorine pesticides in lake water and wastewater
Authors: Lü Jianxia , Liu Jingfu , Wei Yang , Jiang Kaili , Fan Shoushan , Liu Jiyan , Jiang Guibin
Published: July 2007

The feasibility of single‐walled carbon nanotubes (SWCNTs) as adsorbents for solid‐phase microextraction was investigated by using organochlorine pesticides (OCPs) as model compounds. SWCNTs were attached onto a stainless steel wire through organic binder. Potential factors affecting the extraction efficiency were optimized, including extraction time, extraction temperature, desorption time, desorption temperature, and salinity. The developed method has a linear range of 2–800 ng/L for most analytes, with coefficients of correlation ranging from 0.9911 to 0.9996, LODs ranged from 0.19 to 3.77 ng/L (S/N = 3), and RSDs in the range of 3.5–13.9% (n = 5). Compared with the commercial PDMS fiber, the SWCNT fiber has better thermal stability (over 350°C) and longer life span (over 150 times). The developed method was applied to determine trace OCPs in lake water and wastewater samples with external standard calibration. Results showed that OCP contamination was very low in these samples, and HCHs were detected in almost all water samples while DDT concentrations were almost under detection limits in these samples. Recoveries obtained at 20 ng/L spiking level were in the range of 88.4–111% for OCPs in lake water. For wastewater samples, however, the recoveries were satisfactory for HCHs (63.6–97.1%) but relatively low for DDTs (44.7–116%) due to the high content of organic matter in wastewater.
Shotgun proteomic analysis of Arabidopsis thaliana leaves
Authors: Lee Joohyun , Garrett Wesley M. , Cooper Bret
Published: July 2007

Two shotgun tandem MS proteomics approaches, multidimensional protein identification technology (MudPIT) and 1‐D gel‐LC‐MS/MS, were used to identify Arabidopsis thaliana leaf proteins. These methods utilize different protein/peptide separation strategies. Detergents not compatible with MudPIT were used with 1‐D gel‐LC‐MS/MS to help enrich for the detection of membrane‐spanning and hydrophobic proteins. By combining the data from all MudPIT and 1‐D gel‐LC‐MS/MS experiments, 2342 nonredundant proteins spanning a broad range of molecular weights and pI values were detected. With the exception of unknown proteins, the distribution of gene ontology (GO) classifications for the detected proteins was similar to that encoded by the genome, which shows that these extraction and separation procedures are useful for a broad proteomic survey of plant cells. Unknown proteins will likely have to be targeted by using additional methods, some of which should be compatible with separation strategies taken here.
Synthesis of Novel Linear PEO‐b‐PS‐b‐PCL Triblock Copolymers by the Combination of ATRP, ROP, and a Click Reaction
Authors: He Xiaohua , Liang Liyuan , Xie Meiran , Zhang Yiqun , Lin Shaoliang , Yan Deyue
Published: July 2007

A new strategy to synthesize a series of well‐defined amphiphilic PEO‐b‐PS‐b‐PCL block copolymers is presented. First, bromine‐terminated diblock copolymers PEO‐b‐PS‐Br are prepared by ATRP of styrene, and converted into azido‐terminated PEO‐b‐PS‐N3 diblock copolymers. Then propargyl‐terminated PCL is prepared by ROP of ε‐caprolactone. The PEO‐b‐PS‐b‐PCL triblock copolymers with $\overline M _{\rm n}$ from 1.62 × 104 to 1.96 × 104 and a narrow PDI from 1.09 to 1.19 are finally synthesized from these precursors. The structures of these triblock copolymers and their precursors have been characterized by NMR, IR, and GPC analysis.

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A Water‐Soluble π‐Conjugated Polymer with up to 100 mg · mL−1 Solubility
Authors: Wang Huiping , Lu Ping , Wang Baoling , Qiu Song , Liu Meirong , Hanif Muddasir , Cheng Gang , Liu Shiyong , Ma Yuguang
Published: July 2007

A cationic water‐soluble polyfluorene (P2) containing a high density of tetraalkylammonium side chains in polymer backbone was synthesized and characterized. The polymer shows excellent water solubility up to 100 mg · mL−1 as well as high photoluminescence (PL) quantum yield of 44% in water. The relatively high cationic density and appropriate side chain length of the polymer are the key factors to achieve such high water solubility. The reduction potential of P2 is decreased as compared with its neutral polymer, reflecting the enhanced electron injection abilities. The standard NPB/Alq3 device using such a polymer as the electron injection layer shows nearly three‐fold enhancement in the electroluminescence (EL) efficiency.

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Broadband planer array with switchable polarizations
Authors: Bombale Uttam L. , Gupta Sanjeev
Published: July 2007

In this article microstrip planar array of eight elements is designed and simulated. It operates in the frequency range from 3.7 to 4.2 GHz. It gives gain of 17 dB. It can produce many types of polarizations such as Eθ, EΦ, right, and left circular. In all these polarizations the cross‐polar level is around 20 dB lower than the copolar level (except for Eθ, for Eθ it is around 10 dB). The novel microstrip antenna element used in this article is constructed using parasitic patch and shorting pins. It gives wide bandwidth and various polarizations due to parasitic patch and shorting pins, respectively. The array is simulated using Agilent's ADS 2003A momentum software. © 2007 Wiley Periodicals, Inc. Microwave Opt Technol Lett 49: 2415–2419, 2007; Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/mop.22731
Left‐handed characteristic analysis of a split‐ring resonator defected ground structure transmisson line
Authors: Wu Bian , Li Gang , Lai Xin , Liang Chang‐hong
Published: July 2007

The left‐handed properties of a split‐ring resonator defected ground structure transmission line (TL) is investigated in this article. Then the transmission zero location, dispersion relation, impedance characteristic as well as refraction index are derived in detail. The numerical and measurement results validate that, this type of TL unit has the left‐handed properties with transmission zero. © 2007 Wiley Periodicals, Inc. Microwave Opt Technol Lett 49: 2599–2602, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.22752
Does a representative volume element exist for fatigue life prediction? The case of aggregate composites
Authors: Lachihab Adel , Sab Karam
Published: July 2007

In a previous work, discrete modeling and a statistical approach were used to quantify the minimal representative volume element (RVE) size for aggregate composites, such as bituminous materials in the linear elastic regime (Comput. Mater. Sci. 2005; 33:467–490). In this paper, the discrete model is extended to strain‐softening behavior under cyclic loading. The existence of a RVE for fatigue life prediction is numerically proved and its minimal size is determined. It is found that it is much larger than the minimal RVE size in the elastic regime. Copyright © 2007 John Wiley & Sons, Ltd.
Parallel coarse‐grid selection
Authors: Alber David M. , Olson Luke N.
Published: July 2007

Algebraic multigrid (AMG) is a powerful linear solver with attractive parallel properties. A parallel AMG method depends on efficient, parallel implementations of the coarse‐grid selection algorithms and the restriction and prolongation operator construction algorithms. In the effort to effectively and quickly select the coarse grid, a number of parallel coarsening algorithms have been developed. This paper examines the behaviour of these algorithms in depth by studying the results of several numerical experiments. In addition, new parallel coarse‐grid selection algorithms are introduced and tested. Copyright © 2007 John Wiley & Sons, Ltd.
State estimation in process tomography—Three‐dimensional impedance imaging of moving fluids
Authors: Seppänen A. , Vauhkonen M. , Vauhkonen P. J. , Voutilainen A. , Kaipio J. P.
Published: July 2007

In this paper, we consider three‐dimensional impedance imaging of rapidly varying objects. We especially concentrate on the case where the target is a moving fluid and the objective is to track the concentration distribution of a substance dissolved in the fluid. The observations are made as in ordinary electrical impedance tomography (EIT), but in the reconstruction we employ the convection–diffusion model to yield information on the temporal behavior of the object. The observation model of EIT together with the evolution model constitute the state‐space representation of the system, and the reconstruction problem of EIT can be described as a state estimation problem. The state estimation problem is solved using the Kalman filter and the fixed‐interval smoother algorithms. The performance of the state estimation approach is evaluated in a simulation study. Copyright © 2007 John Wiley & Sons, Ltd.
Blends of starch with ethylene vinyl alcohol copolymers: effect of water, glycerol, and amino acids as plasticizers
Authors: Orts William J. , Nobes Geoffrey A. R. , Glenn Gregory M. , Gray Gregory M. , Imam Syed , Chiou Bor‐Sen
Published: July 2007

Blends of thermoplastic starch with poly(ethylene‐co‐vinyl alcohol) copolymer (EVOH) were melt extruded with water/glycerol as plasticizer and a series of amino acid additives. The biggest factor in end‐use mechanical properties proved to be the relative humidity (RH) during storage. Plasticized starch‐EVOH blends stored at 0 and 50% RH changed significantly over time, with, for example, the tensile strength (TS) of the glycerol‐plasticized blend increasing from 4.7 to 26.3 MPa over 8 weeks when maintained at 0% RH. In contrast, the TS of this same sample stored at 75% RH remained unchanged for 8 weeks. Amino acids provided relatively minor, but significant changes in mechanical properties with time. Based on TS, elongation‐to‐break, and modulus, it may be concluded that β‐alanine, sarcosine, and L‐proline were more effective than glycerol at maintaining strong flexible blends. Increases in crystallinity and changes in morphology with time, as described by modulated DSC were correlated to these changes in mechanical properties. Published in 2007 by John Wiley & Sons, Ltd.
Molecular basis of LFER: theoretical study of polar substituent effect in aliphatic series
Authors: Ponec Robert , Van Damme Sofie
Published: July 2007

The nature of inductive substituent effect on the gas phase acidity of several series of aliphatic carboxylic acids with rigid molecular skeletons was analyzed using the recently proposed quantum chemical approach based on the theory of proton affinity proposed by Longuet‐Higgins. The results of the analysis suggest that the substituent induced variation of the acidity is in all series due to electrostatic field‐effect which in the gas phase can reasonably be characterized by Kirkwood–Westheimer theory. Copyright © 2007 John Wiley & Sons, Ltd.
Ketene‐forming elimination reactions from aryl phenylacetates promoted by R2NH in MeCN: effects of base‐solvent and β‐phenyl group
Authors: Pyun Sang Yong , Seok Hyoun Jung , Kim Ju Chang , Kim Hwan Myung , Cho Bong Rae
Published: July 2007

Elimination reactions of C6H5C(R)HCO2C6H3‐2‐X‐4‐NO2 [R = H (1), Ph (2), X = H (a), Cl (b), NO2 (c)] promoted by R2NH in MeCN have been studied kinetically. The reactions are second‐order and exhibit Brönsted β = 0.46–0.89 and |βlg| = 0.37–0.76 and an E2 mechanism is evident. When the base‐solvent was changed from R2NH/R2NH–70 mol% MeCN(aq) to R2NH‐MeCN, β and |βlg| values remained nearly the same within experimental error. For eliminations from 1 and 2, β and |βlg| values were nearly identical, although the rate was retarded by the β‐Ph group. Noteworthy is the relative insensitivity of the ketene‐forming transition state to the base‐solvent and β‐R group variation. Copyright © 2007 John Wiley & Sons, Ltd.
Crystal structure of MtnX phosphatase from Bacillus subtilis at 2.0 Å resolution provides a structural basis for bipartite phosphomonoester hydrolysis of 2‐hydroxy‐3‐keto‐5‐methylthiopentenyl‐1‐phosphate
Authors: Xu Qingping , Saikatendu Kumar Singh , Krishna S. Sri , McMullan Daniel , Abdubek Polat , Agarwalla Sanjay , Ambing Eileen , Astakhova Tamara , Axelrod Herbert L. , Carlton Dennis , Chiu Hsiu‐Ju , Clayton Thomas , DiDonato Michael , Duan Lian , Elsliger Marc‐André , Feuerhelm Julie , Grzechnik Slawomir K. , Hale Joanna , Hampton Eric , Han Gye Won , Haugen Justin , Jaroszewski Lukasz , Jin Kevin K. , Klock Heath E. , Knuth Mark W. , Koesema Eric , Miller Mitchell D. , Morse Andrew T. , Nigoghossian Edward , Okach Linda , Oommachen Silvya , Paulsen Jessica , Reyes Ron , Rife Christopher L. , Schwarzenbacher Robert , van den Bedem Henry , White Aprilfawn , Wolf Guenter , Hodgson Keith O. , Wooley John , Deacon Ashley M. , Godzik Adam , Lesley Scott A. , Wilson Ian A.
Published: July 2007

No abastract.