bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dual‐level direct dynamics studies for the reactions of OH radical with bromine‐substituted ethanes
Authors: Wang Li , Liu Jing‐yao , Gao Hong , Wan Su‐qin , Li Ze‐sheng 
Published: September 2008

AbstractThe dynamic properties of the multichannel hydrogen abstraction reactions of CH3CH2Br + OH → products and CH3CHBr2 + OH → products are studied by dual‐level direct dynamics method. For each reaction, three reaction channels, one for α‐hydrogen abstraction and two for β‐hydrogen abstractions, have been identified. The minimum energy paths (MEPs) of both the reactions are calculated at the Becke's half‐and‐half (BH&H)‐Lee‐Yang‐Parr (LYP)/6‐311G(d, p) level and the energy profiles along the MEPs are further refined with interpolated single‐point energies (ISPE) method at the G2M(RCC5)//BH&H‐LYP level. There are complexes with energies less than those of the reactants or products located at the entrance or exit channels, which indicates that the reactions may proceed via an indirect mechanism. By canonical variational transition‐state theory (CVT) the rate constants are calculated incorporating the small‐curvature tunneling (SCT) correction in the temperature range of 220–2000 K. The agreement of the rate constants with available experimental values for two reactions is good in the measured temperature range. The calculated results show that α‐hydrogen abstraction channel is the major reaction pathway in the lower temperature for two reactions, while the contribution of β‐hydrogen abstraction will increase with the increase in temperature. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009
Comments on the molecular geometry of ferrocene: The dangers of using quantum chemistry programs as black boxes
Authors: Martin Jason , Baker Jon , Pulay Peter 
Published: September 2008

AbstractThe dangers of using standard quantum chemistry programs as black boxes is illustrated by analyzing some results in a recent paper published in this journal (Zhang et al., J Comput Chem 2007, 28, 2260). The main danger is that nonlinear optimizations of both the wavefunction and the molecular geometry may converge to higher local minima or to saddle points, producing misleading results. For instance, some of the calculated molecular geometries of ferrocene in the aforementioned paper correspond to an SCF solution that converged to an excited state. This is the cause of the apparent large variation in the calculated iron‐ring distance with the basis set. Another problem we noticed is that the source of the diffuse functions used in the earlier work in connection with the 6‐31G and 6‐311G basis sets for transition metals is not specified in the literature or the program manual. They are also a poor match for the 6‐31G basis set. We re‐emphasize that the 6‐31G basis set used in this paper lacks the necessary diffuse d‐type functions for the late first‐row transition metals, and ought to be replaced by the m6‐31G basis that offers a more balanced description of the atomic valence states. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Mesoscopic model for mechanical characterization of biological protein materials
Authors: Yoon Gwonchan , Park Hyeong‐Jin , Na Sungsoo , Eom Kilho 
Published: September 2008

AbstractMechanical characterization of protein molecules has played a role on gaining insight into the biological functions of proteins, because some proteins perform the mechanical function. Here, we present the mesoscopic model of biological protein materials composed of protein crystals prescribed by Go potential for characterization of elastic behavior of protein materials. Specifically, we consider the representative volume element (RVE) containing the protein crystals represented by Cα atoms, prescribed by Go potential, with application of constant normal strain to RVE. The stress–strain relationship computed from virial stress theory provides the nonlinear elastic behavior of protein materials and their mechanical properties such as Young's modulus, quantitatively and/or qualitatively comparable with mechanical properties of biological protein materials obtained from experiments and/or atomistic simulations. Further, we discuss the role of native topology on the mechanical properties of protein crystals. It is shown that parallel strands (hydrogen bonds in parallel) enhance the mechanical resilience of protein materials. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Discoidin domain receptor 1 activation suppresses α2β1 integrin‐dependent cell spreading through inhibition of Cdc42 activity
Authors: Yeh Yi‐Chun , Wang Chau‐Zen , Tang Ming‐Jer 
Published: September 2008

AbstractUpregulation and overexpression of discoidin domain receptor 1 (DDR1) have been implied in the regulation of kidney development and progression of cancers. Our previous studies with Mardin–Darby canine kidney (MDCK) cells showed that overexpression of DDR1 inhibited cell spreading, whereas dominant negative DDR1 promoted cell spreading on collagen‐coated dish. Cell spreading is an important characteristic for cell differentiation and survival. However, little is known about the molecular mechanisms underlying the role of DDR1 in cell spreading. We have found here a novel signaling pathway of DDR1 consisting of Cdc42 that regulates the assembly and disassembly of cytoskeleton and cell spreading in MDCK cells. Cell spreading involves the organization of cytoskeleton that is mainly regulated by Rho‐family GTPases. We assessed the activity of Rho‐family GTPases and transfected MDCK cells with constitutively active or dominant negative GTPases, and quantified the extent of cell spreading. These results showed that DDR1 decreased the filamentous actin ratio and Rac1/Cdc42 activities, but had no effects on RhoA activity. Neither constitutively active nor dominant negative Rac1 altered DDR1‐inhibited cell spreading. Constitutively active Cdc42 could rescue the DDR1‐inhibited cell spreading, whereas dominant negative Cdc42 inhibited cell spreading, indicating that DDR1‐inhibited cell spreading is Cdc42 dependent. With the use of α2β1 integrin blocking antibody, we showed that collagen‐induced Cdc42 activation was mediated by α2β1 integrin. Moreover, ectopic FAK expression enhanced the Cdc42 activity. Reducing FAK activity by dominant negative FAK (FRNK) markedly abolished the Cdc42 activity. These findings show that DDR1a/b activation inhibits cell spreading through suppressing α2β1 integrin‐mediated Cdc42 activation. J. Cell. Physiol. 218: 146–156, 2009. © 2008 Wiley‐Liss, Inc.
Breast filariasis: Real‐time sonographic imaging of the filarial dance
Authors: Surendrababu Narayanam R.S. , Thomas Elsa , Rajinikanth Janakiraman , Keshava Shyamkumar N. 
Published: September 2008

AbstractA 50‐year‐old woman presented with a palpable tender nodule in the upper quadrant of the breast that was clinically thought to be a fibroadenoma, with mammographic findings of a well‐defined lobulated density. Sonographic examination revealed a “filarial dance sign” within the cystic lesion, which is diagnostic of lymphatic breast filariasis. In endemic areas, sonographic examination is recommended to search for this pathognomonic real‐time diagnostic feature and, if present, to initiate treatment without delay. © 2008 Wiley Periodicals, Inc. J Clin Ultrasound, 2008
Parallel imaging enhanced MR colonography using a phantom model
Authors: Morrin Martina M. , Pedrosa Ivan , McKenzie Charles A. , Farrell Richard J. , Bloch Nicolas , Solazzo Stephanie , Ngo Long , Goldberg Shraga N. , Rofsky Neil M. 
Published: September 2008

AbstractPurposeTo compare various Array Spatial and Sensitivity Encoding Technique (ASSET)‐enhanced T2W SSFSE (single shot fast spin echo) and T1‐weighted (T1W) 3D SPGR (spoiled gradient recalled echo) sequences for polyp detection and image quality at MR colonography (MRC) in a phantom model. Limitations of MRC using standard 3D SPGR T1W imaging include the long breath‐hold required to cover the entire colon within one acquisition and the relatively low spatial resolution due to the long acquisition time. Parallel imaging using ASSET‐enhanced T2W SSFSE and 3D T1W SPGR imaging results in much shorter imaging times, which allows for increased spatial resolution.Materials and MethodsUsing two porcine colon phantoms each with eight simulated 3–10‐mm “polyps,” baseline reference sequences acquired without ASSET (6‐mm slices and readout bandwidth [BW] 62 kHz) were compared with 11 SSFSE and 8 SPGR sequences acquired with 2‐fold ASSET acceleration. ASSET‐enhanced SSFSE and SPGR sequences comprised BW/matrix combinations ranging from 20–62 kHz / 256–352 × 256, respectively, with slice thicknesses adjusted from 3.0 to 4.5 mm to maintain a 23–26‐second acquisition time and 30 cm slab thickness. Two experienced radiologists viewed the datasets in a randomized, blinded fashion.ResultsCompared to reference sequences, ASSET‐enhanced SSFSE and SPGR sequences facilitated better polyp detection and had similar overall image quality and per‐phantom specificity. The two best ASSET‐enhanced SSFSE (3 and 4.5 mm slices, each with BW of 62.5 kHz and 352 × 256 matrices) and three best ASSET‐enhanced SPGR BW / slice thickness / matrix combinations of 31 kHz / 4.4 msec / 192 × 256; 62 / 3.4 / 192 × 256; and 62 / 4.0 / 192 × 256, respectively, permitted detection of all polyps ≥5 mm.ConclusionParallel imaging using ASSET‐enhanced T2W SSFSE and T1W 3D SPGR improves the ability to detect significant colon polyps in an MRC phantom model. J. Magn. Reson. Imaging 2008;28:664–672. © 2008 Wiley‐Liss, Inc.
MRI diagnosis of brown tumor based on magnetic susceptibility
Authors: Knowles Negar G. , Smith Deven L. , Outwater Eric K. 
Published: September 2008

AbstractA 56‐year‐old male with chronic renal failure was incidentally found to have lytic bone lesions in the pubic symphysis, left femoral head, left acetabulum, left iliac bone, and L1 vertebra on computed tomography (CT). Subsequent magnetic resonance imaging (MRI) of the abdomen was performed (for evaluation of a renal lesion) which demonstrated marked loss of signal intensity in the L1 bone lesion on increasing TE gradient echo images, consistent with magnetic susceptibility effect due to hemosiderin. Brown tumor was confirmed at biopsy. The susceptibility imaging probes one particular histological characteristic of tissues and allows a restricted differential of lytic tumors that contain significant hemosiderin, including brown tumor. J. Magn. Reson. Imaging 2008;28:759–761. © 2008 Wiley‐Liss, Inc.
T1ρ‐prepared balanced gradient echo for rapid 3D T1ρ MRI
Authors: Witschey Walter R.T. , Borthakur Arijitt , Elliott Mark A. , Fenty Matthew , Sochor Matthew A. , Wang Chenyang , Reddy Ravinder 
Published: September 2008

AbstractPurposeTo develop a T1ρ‐prepared, balanced gradient echo (b‐GRE) pulse sequence for rapid three‐dimensional (3D) T1ρ relaxation mapping within the time constraints of a clinical exam (<10 minutes), examine the effect of acquisition on the measured T1ρ relaxation time and optimize 3D T1ρ pulse sequences for the knee joint and spine.Materials and MethodsA pulse sequence consisting of inversion recovery–prepared, fat saturation, T1ρ‐preparation, and b‐GRE image acquisition was used to obtain 3D volume coverage of the patellofemoral and tibiofemoral cartilage and lower lumbar spine. Multiple T1ρ‐weighted images at various contrast times (spin‐lock pulse duration [TSL]) were used to construct a T1ρ relaxation map in both phantoms and in the knee joint and spine in vivo. The transient signal decay during b‐GRE image acquisition was corrected using a k‐space filter. The T1ρ‐prepared b‐GRE sequence was compared to a standard T1ρ‐prepared spin echo (SE) sequence and pulse sequence parameters were optimized numerically using the Bloch equations.ResultsThe b‐GRE transient signal decay was found to depend on the initial T1ρ‐preparation and the corresponding T1ρ map was altered by variations in the point spread function with TSL. In a two compartment phantom, the steady state response was found to elevate T1ρ from 91.4 ± 6.5 to 293.8 ± 31 and 66.9 ± 3.5 to 661 ± 207 with no change in the goodness‐of‐fit parameter R2. Phase encoding along the longest cartilage dimension and a transient signal decay k‐space filter retained T1ρ contrast. Measurement of T1ρ using the T1ρ‐prepared b‐GRE sequence matches standard T1ρ‐prepared SE in the medial patellar and lateral patellar cartilage compartments. T1ρ‐preparedb‐GRE T1ρ was found to have low interscan variability between four separate scans. Mean patellar cartilage T1ρ was elevated compared to femoral and tibial cartilage T1ρ.ConclusionThe T1ρ‐prepared b‐GRE acquisition rapidly and reliably accelerates T1ρ quantification of tissues offset partially by a TSL‐dependent point spread function. J. Magn. Reson. Imaging 2008;28:744–754. © 2008 Wiley‐Liss, Inc.
Mapping of vertebral artery perfusion territories using arterial spin labeling MRI
Authors: Kansagra Akash P. , Wong Eric C. 
Published: September 2008

AbstractPurposeTo demonstrate the use of a noninvasive arterial spin labeling (ASL) MRI technique and evaluate vertebral artery (VA) territories in the brain.Materials and MethodsVessel‐encoded ASL was used to determine the territories of the left and right VAs in five healthy subjects. Territory maps were analyzed quantitatively by comparing the fractional contributions of the left and right VAs in selected regions of interest within the brain.ResultsVA territory maps demonstrated a complicated pattern of perfusion to the posterior aspect of the brain, but were consistent with the posterior cerebral and cerebellar artery distributions. Cerebellar perfusion was predominantly ipsilateral (P < 0.01). The total left and right VA contributions were unequal (P < 0.01), and there was relatively little mixing in the vertebrobasilar system.ConclusionVessel‐encoded ASL can reveal individual VA territories in the brain. In a small sample of healthy volunteers the VAs appeared to contribute unequally, provide predominantly ipsilateral supply to the cerebellum, and undergo minimal mixing in the basilar artery. J. Magn. Reson. Imaging 2008;28:762–766. © 2008 Wiley‐Liss, Inc.
Fast projective carotid MR angiography using arterial spin‐labeled balanced SSFP
Authors: Koktzoglou Ioannis , Edelman Robert R. 
Published: September 2008

AbstractPurposeTo determine whether pulsed arterial spin‐labeled (pulsed ASL) balanced steady‐state free precession (bSSFP) imaging allows for rapid projective depiction of the carotid arteries without electrocardiographic (ECG) gating.Materials and MethodsThe carotid arteries of six volunteers were scanned at 1.5 T using an ASL two‐dimensional bSSFP sequence. Three configurations were tested, with and without ECG gating: (a) full field‐of‐view (FOV) acquisition (scan time = 48 s), (b) full‐FOV acquisition with parallel acceleration of 2 (24 s), and sequence C (half‐FOV acquisition (24 s). Vessel‐to‐background contrast‐to‐noise ratios (CNRs) and vessel lengths were compared between sequence configurations. Vessel caliber measurements were compared with those obtained from three‐dimensional time‐of‐flight (TOF) angiography.ResultsThe carotid arteries were seen over extensive lengths with ASL two‐dimensional bSSFP. Projected vessel length and vessel‐to‐background CNR did not differ with ECG gating (P = NS). Nonaccelerated full‐FOV and half‐FOV scans provided larger apparent vessel‐to‐background CNR and slightly longer vessel lengths than the parallel‐accelerated scans (P < 0.01). Carotid diameter measurements were in agreement with those obtained from three‐dimensional TOF (intraclass correlation coefficient = 0.810; P < 0.001).Conclusionpulsed ASL bSSFP is a fast technique for projective carotid angiography that may not require ECG gating. Acquisition time may be decreased with reduced FOV or parallel imaging strategies. J. Magn. Reson. Imaging 2008;28:778–782. © 2008 Wiley‐Liss, Inc.
Dixon techniques for water and fat imaging
Authors: Ma Jingfei 
Published: September 2008

AbstractIn 1984, Dixon published a first paper on a simple spectroscopic imaging technique for water and fat separation. The technique acquires two separate images with a modified spin echo pulse sequence. One is a conventional spin echo image with water and fat signals in‐phase and the other is acquired with the readout gradient slightly shifted so that the water and fat signals are 180° out‐of‐phase. Dixon showed that from these two images, a water‐only image and a fat‐only image can be generated. The water‐only image by the Dixon's technique can serve the purpose of fat suppression, an important and widely used imaging option for clinical MRI. Additionally, the availability of both the water‐only and fat‐only images allows direct image‐based water and fat quantitation. These applications, as well as the potential that the technique can be made highly insensitive to magnetic field inhomogeneity, have generated substantial research interests and efforts from many investigators. As a result, significant improvement to the original technique has been made in the last 2 decades. The following article reviews the underlying physical principles and describes some major technical aspects in the development of these Dixon techniques. J. Magn. Reson. Imaging 2008;28:543–558. © 2008 Wiley‐Liss, Inc.
Double‐reference cross‐correlation algorithm for separation of the arteries and veins from 3D MRA time series
Authors: Santini Francesco , Patil Sunil , Meckel Stephan , Scheffler Klaus , Wetzel Stephan G. 
Published: September 2008

AbstractPurposeTo present a novel postprocessing technique for artery/vein separation and background suppression from contrast‐enhanced time‐resolved magnetic resonance angiography datasets in order to improve the diagnosis of vessel pathologies and arteriovenous fistulas.Materials and MethodsTen normal, two pathologic datasets of the brain, and one hand angiography dataset were postprocessed. Cross‐correlation maps between the signal time course of every voxel in the dataset and selected arterial and venous references regions of interest (ROIs) were obtained; these maps were subsequently nonlinearly transformed to obtain two indices representing the likelihood of a voxel belonging to a vessel category. Red‐green‐blue (RGB) color encoding was utilized to depict synthetic arteriogram and venogram images in a single diagnostically meaningful image.ResultsThe technique enabled correct visual separation of vessels on various datasets, as evaluated by two expert neuroradiologists, and also highlighted characteristics of flow in arteriovenous fistulas. A quantitative comparison with existing techniques showed better separation performance on 3 out of 10 normal datasets and higher stability to acquisition characteristics and contrast agent bolus dispersion.ConclusionThis method can be helpful in the diagnosis of vascular diseases in subjects where bolus dispersion makes it difficult to discriminate between arteries and veins with standard methods (subtraction or correlation analysis). J. Magn. Reson. Imaging 2008;28:646–654. © 2008 Wiley‐Liss, Inc.
Free‐breathing, nongated real‐time delayed enhancement MRI of myocardial infarcts: A comparison with conventional delayed enhancement
Authors: Detsky Jay S. , Graham John J. , Vijayaraghavan Ram , Biswas Labonny , Stainsby Jeffrey A. , Guttman Michael A. , Wright Graham A. , Dick Alexander J. 
Published: September 2008

AbstractPurposeTo compare a free‐breathing, nongated, and black‐blood real‐time delayed enhancement (RT‐DE) sequence to the conventional inversion recovery gradient echo (IR‐GRE) sequence for delayed enhancement MRI.Materials and MethodsTwenty‐three patients with suspected myocardial infarct (MI) were examined using both the IR‐GRE and RT‐DE imaging sequences. The sensitivity and specificity of RT‐DE for detecting MI, using IR‐GRE as the gold standard, was determined. The contrast‐to‐noise ratios (CNR) between the two techniques were also compared.ResultsRT‐DE had a high sensitivity and specificity (94% and 98%, respectively) for identifying MI. The total acquisition time to image the entire left ventricle was significantly shorter using RT‐DE than IR‐GRE (5.6 ± 0.9 versus 11.5 ± 1.9 min). RT‐DE had a slightly lower infarct‐myocardium CNR but a higher infarct‐blood CNR than IR‐GRE imaging. Compared with IR‐GRE, RT‐DE accurately measured total infarct sizes.ConclusionRT‐DE can be used for delayed enhancement imaging during free‐breathing and without cardiac gating. J. Magn. Reson. Imaging 2008;28:621–625. © 2008 Wiley‐Liss, Inc.
Gadobenate dimeglumine–enhanced magnetic resonance imaging of primary leiomyoma of the liver
Authors: Marin Daniele , Catalano Carlo , Rossi Massimo , Guerrisi Antonino , Di Martino Michele , Berloco Pasquale , Passariello Roberto 
Published: September 2008

AbstractWe report a case of histologically proven primary leiomyoma of the liver that was evaluated with multiphasic 64‐section computed tomography (CT) and gadobenate dimeglumine–enhanced magnetic resonance (MR) imaging. This lesion showed vivid enhancement during the arterial phase with sustained enhancement during the hepatic venous and equilibrium phases. During the liver‐specific MR imaging phase (150 minutes after contrast injection), the same lesion demonstrated lack of contrast retention, thus appearing hypointense compared with the background liver. Because of this latter finding, the patient underwent partial resection of the liver. In primary hepatic leiomyoma, the absence of contrast uptake during the liver‐specific phase of gadobenate dimeglumine–enhanced MR imaging may be inappropriately interpreted as a sign of malignancy, thus leading to unnecessary, aggressive management of such lesions. J. Magn. Reson. Imaging 2008;28:755–758. © 2008 Wiley‐Liss, Inc.
Modifications of the DC Raytheon–Statz model for SiC MESFETs
Authors: Zarębski Janusz , Bisewski Damian 
Published: September 2008

AbstractIn the paper the problem of modelling DC characteristics of SiC MESFETs is presented. Some modifications of the popular Raytheon–Statz model built‐in in SPICE are proposed. The original and the modified models are verified experimentally by comparison of the measured and simulated device characteristics. One of the two available today on the market SiC MESFETs–the transistor CRF24010 offered by Cree, Inc. is chosen for investigations. Copyright © 2008 John Wiley & Sons, Ltd.
Concentration‐ and temperature‐dependent conformation change of cyclohexyl isocyanide on gold nanoparticle surfaces
Authors: Joo Sang‐Woo , Kang Weekyung , Oh Jeong Jin 
Published: September 2008

AbstractThe conformational changes of cyclohexyl isocyanide (CHNC) on gold nanoparticle surfaces were investigated by means of concentration‐ and temperature‐dependent surface‐enhanced Raman scattering (SERS). The equatorial chair conformer appeared to be dominant at high‐bulk concentrations or low temperatures, whereas both the equatorial and axial chair conformers of CHNC were found to exist at low‐bulk concentrations or high temperatures as in the previous reports of cyclohexanethiol (CHT). Depending on concentrations and temperatures, the spectral changes of the NC stretching vibration on gold nanoparticles appeared to be more conspicuous than those of the cyclohexyl ring modes. A density functional theory (DFT) calculation was performed at the level of B3LYP/6‐31G + + (d,p) to compare the energetic stability of the various conformers of CHT and CHNC. The energy differences between the equatorial and axial chair conformers were predicted to be smaller for CHNC than for CHT by ∼3 kJ mol−1 from the DFT calculation. Copyright © 2008 John Wiley & Sons, Ltd.