bluuebunny/crossref_metadata_2025 huggingface dataset:
MR‐guided radiofrequency ablation in a 0.2‐T open MR system: Technical success and technique effectiveness in 100 liver tumors
Authors: Clasen Stephan , Boss Andreas , Schmidt Diethard , Schraml Christina , Fritz Jan , Schick Fritz , Claussen Claus D. , Pereira Philippe L.
Published: September 2007

Purpose

To evaluate the feasibility and technique effectiveness of magnetic resonance (MR)‐guided radiofrequency (RF) ablation of hepatic malignancies.

Materials and Methods

In 64 patients, 100 primary (N = 19) or secondary (N = 81) liver tumors (mean diameter = 24.7 mm; range = 4–60 mm) were treated with 87 sessions of MR‐guided RF ablation. The entire ablation procedure was carried out at an 0.2‐T open MR system by using MR‐compatible internally cooled electrodes. T2‐weighted turbo spin echo sequences (TR/TE = 3500 msec/110 msec) were used to monitor thermally induced coagulation. Technique effectiveness was assessed four months after the last RF ablation by dynamic MR imaging at 1.5‐T.

Results

MR‐guided RF ablation procedures were technical successful in 85 of 87 (97.7%) assessed at the end of each session. Complete coagulation was intended in 99 of 100 tumors. Technique effectiveness was observed in 92 of 99 (92.9%) of these tumors. To achieve complete coagulation 82 of 92 (89.1%) tumors required a single session. T2‐weighted sequences were accurate to monitor the extent of coagulation and were supportive to guide overlapping ablation. There were two of 87 (2.3%) major and seven of 87 (8.0%) minor complications.

Conclusion

MR‐guided RF ablation is a safe and effective therapy in the treatment of hepatic malignancies. MR imaging offers an accurate monitoring of thermally‐induced coagulation, thus enabling complete tumor coagulation in a single session. J. Magn. Reson. Imaging 2007;26:1043–1052. © 2007 Wiley‐Liss, Inc.
Parallel imaging of knee cartilage at 3 Tesla
Authors: Zuo Jin , Li Xiaojuan , Banerjee Suchandrima , Han Eric , Majumdar Sharmila
Published: September 2007

Purpose

To evaluate the feasibility and reproducibility of quantitative cartilage imaging with parallel imaging at 3T and to determine the impact of the acceleration factor (AF) on morphological and relaxation measurements.

Materials and Methods

An eight‐channel phased‐array knee coil was employed for conventional and parallel imaging on a 3T scanner. The imaging protocol consisted of a T2‐weighted fast spin echo (FSE), a 3D‐spoiled gradient echo (SPGR), a custom 3D‐SPGR T1rho, and a 3D‐SPGR T2 sequence. Parallel imaging was performed with an array spatial sensitivity technique (ASSET). The left knees of six healthy volunteers were scanned with both conventional and parallel imaging (AF = 2).

Results

Morphological parameters and relaxation maps from parallel imaging methods (AF = 2) showed comparable results with conventional method. The intraclass correlation coefficient (ICC) of the two methods for cartilage volume, mean cartilage thickness, T1rho, and T2 were 0.999, 0.977, 0.964, and 0.969, respectively, while demonstrating excellent reproducibility. No significant measurement differences were found when AF reached 3 despite the low signal‐to‐noise ratio (SNR).

Conclusion

The study demonstrated that parallel imaging can be applied to current knee cartilage quantification at AF = 2 without degrading measurement accuracy with good reproducibility while effectively reducing scan time. Shorter imaging times can be achieved with higher AF at the cost of SNR. J. Magn. Reson. Imaging 2007;26:1001–1009. © 2007 Wiley‐Liss, Inc.
Cancer yield of probably benign breast MR examinations
Authors: Eby Peter R. , DeMartini Wendy B. , Peacock Sue , Rosen Eric L. , Lauro Bridget , Lehman Constance D.
Published: September 2007

Purpose

To evaluate the cancer yield, frequency of use, and follow‐up compliance of breast MR examinations assessed as “probably benign.”

Materials and Methods

We retrospectively reviewed our MR database of 809 consecutive examinations between January 2003 and June 2004. We identified all examinations that ultimately received an MR breast imaging reporting and data system (BI‐RADS) 3 assessment and recommendation for a short‐interval follow‐up MR with or without an antecedent targeted ultrasound. The clinical indication for breast MR, date of the follow‐up examination, follow‐up assessment, and any pathology findings through June 2005 were collected from clinical records and radiology and pathology reports. Frequency of BI‐RADS 3 use, follow‐up compliance, and cancer yield were calculated.

Results

A total of 160 out of 809 (20%) examinations comprise the study population. A total of 100 out of 160 (63%) women returned for the recommended follow‐up MR, in which three out of 100 (3%) were upgraded to BI‐RADS 4 with biopsy recommended. One patient underwent biopsy and the result was benign. A total of seven out of 160 (4%) underwent mastectomy in lieu of MR for known cancer elsewhere in the breast. One out of seven mastectomy specimens contained malignancy that corresponded to the probably benign finding, resulting in a cancer yield of one out of 160 (0.6%).

Conclusion

Our data suggest that follow‐up MR is a valid alternative to biopsy for MR BI‐RADS 3 lesions. J. Magn. Reson. Imaging 2007;26:950–955. © 2007 Wiley‐Liss, Inc.
Gadobenate dimeglumine‐enhanced MR angiography: Diagnostic performance of four doses for detection and grading of carotid, renal, and aorto‐iliac stenoses compared to digital subtraction angiography
Authors: Schneider Günther , Ballarati Claudio , Grazioli Luigi , Manfredi Riccardo , Thurnher Siegfried , Kroencke Thomas J. , Taupitz Matthias , Merlino Biagio , Bonomo Lorenzo , Shen Ningyan , Pirovano Gianpaolo , Kirchin Miles A. , Spinazzi Alberto
Published: September 2007

Purpose

To determine the diagnostic performance of contrast‐enhanced MR angiography (CE‐MRA) with four doses of gadobenate dimeglumine for detection of significant steno‐occlusive disease of the carotid, renal, and pelvic vasculature.

Materials and Methods

Eighty‐four patients with suspected disease of the renal (n = 16), pelvic (n = 41), or carotid (n = 27) arteries underwent CE‐MRA (3D‐spoiled gradient‐echo sequences) at 1.5T. CE‐MRA was performed with gadobenate dimeglumine at 0.025, 0.05, 0.1, or 0.2 mmol/kg (23, 24, 19, and 18 patients, respectively) administered at 2 mL/sec. Accuracy, sensitivity, specificity, and positive and negative predictive values (PPV and NPV, respectively) for detection of significant disease (>50% stenosis or occlusion for renal/pelvic arteries; >70% stenosis or occlusion for carotid arteries) was determined by three fully blinded, independent radiologists using conventional digital subtraction angiography (DSA) as reference standard. All comparisons were tested statistically (ANOVA, chi‐square, and Mantel–Haenszel tests as appropriate) and reader agreement (kappa) was assessed.

Results

Values for accuracy, sensitivity, specificity, PPV, and NPV on CE‐MRA were consistently higher for 0.1 mmol/kg gadobenate dimeglumine (accuracy = 95.2–97.3%, sensitivity = 84.2% (all readers), specificity = 96.9–99.2%, PPV = 80.0–94.1%, NPV = 97.6–97.7%). The greater accuracy of the 0.1 mmol/kg dose was significant (P < 0.01, all readers) compared to all other dose groups. Agreement between the three readers was good for all dose groups (kappa ≥0.58), with the highest percent agreement (85.7%) noted for the 0.1 mmol/kg dose.

Conclusion

Significantly better diagnostic performance on CE‐MRA of the renal, pelvic, and carotid arteries is achieved with a gadobenate dimeglumine dose of 0.1 mmol/kg bodyweight. J. Magn. Reson. Imaging 2007;26:1020–1032. © 2007 Wiley‐Liss, Inc.
Improved dynamic susceptibility contrast (DSC)‐MR perfusion estimates by motion correction
Authors: Kosior Robert K. , Kosior Jayme C. , Frayne Richard
Published: September 2007

Purpose

To investigate the effect of patient motion on quantitative cerebral blood flow (CBF) maps in ischemic stroke patients and to evaluate the efficacy of a motion‐correction scheme.

Materials and Methods

Perfusion data from 25 ischemic stroke patients were selected for analysis. Two motion profiles were applied to a digital anthropomorphic brain phantom to estimate accuracy. CBF images were generated for motion‐corrupted and motion‐corrected data. To correct for motion, rigid‐body registration was performed. The realignment parameters and mean CBF in regions of interest were recorded.

Results

All patient data with motion exhibited visibly reduced intervolume misalignment after motion correction. Improved flow delineation between different tissues and a more clearly defined ischemic lesion (IL) were achieved in the motion‐corrected CBF. A significant difference occurred in the IL (P < 0.05) for patients with severe motion with an average difference between corrupted and corrected data of 4.8 mL/minute/100 g. The phantom data supported the patient results with better CBF accuracy after motion correction and high registration accuracy (<1 mm translational and <1° rotational error).

Conclusion

Motion degrades flow differentiation between adjacent tissues in CBF maps and can cause ischemic severity to be underestimated. A registration motion correction scheme improves dynamic susceptibility contrast (DSC)‐MR perfusion estimates. J. Magn. Reson. Imaging 2007;26:1167–1172. © 2007 Wiley‐Liss, Inc.
An examination of the effects of organizational district and team contexts on team processes and performance: a meso‐mediational model
Authors: Mathieu John E. , Maynard M. Travis , Taylor Scott R. , Gilson Lucy L. , Ruddy Thomas M.
Published: September 2007

We examined the effects of organizational district and team contexts on team processes and performance in a longitudinal cross‐level design. As hypothesized, at the team‐level of analysis, interdependence related positively to team performance as partially mediated by processes. Moreover, a cross‐level mediational relationship was evident between the organizational district‐level openness climate and team performance as fully mediated by team processes. In contrast, organizational district‐level multi‐team coordination unexpectedly exhibited a direct cross‐level relationship with team performance. Multi‐team coordination also negatively interacted with team processes as related to team performance, in an exploratory analysis. Results are discussed in terms of the importance of considering both organizational‐district and team contexts as embedding conditions that influence team effectiveness. Copyright © 2007 John Wiley & Sons, Ltd.
Job design in temporal context: a career dynamics perspective
Authors: Fried Yitzhak , Grant Adam M. , Levi Ariel S. , Hadani Michael , Slowik Linda Haynes
Published: September 2007

Leading theories of job design have neglected to incorporate the important context of time into their premises, hindering these theories' explanatory power and utility. We demonstrate how systematically incorporating the context of time, in relation to the specific example of career dynamics, will improve our understanding of job design. We discuss the contribution of time by examining how career dynamics may influence employees' reactions to stimulating jobs and their propensity to craft more stimulating jobs. Copyright © 2007 John Wiley & Sons, Ltd.
Effect of baking method on some characteristics of starch in pound cake crumbs
Authors: Sánchez‐Pardo María E , Ortiz‐Moreno Alicia , Mora‐Escobedo Rosalva , Bello‐Pérez Arturo , Yee‐Madeira Hernani , Ramos‐López Gonzalo
Published: September 2007

BACKGROUND: The effect of the baking process (microwave versus conventional oven) on some starch characteristics of pound cake was evaluated. Proximal chemical analysis, total resistant starch (RS), retrograded resistant starch (RS3), differential scanning calorimetry (DSC), and X‐ray diffraction (XRD) were evaluated. Pound cake, one of the major products of Mexico's bread industry, was selected for analysis because the high moisture and fat content in the beaten dough might reduce the quality defects often associated with microwave baking.

RESULTS: Crumbs from microwave‐baked pound cakes contained lower moisture than crumbs from conventionally baked pound cake. Lower RS was observed in fresh microwave‐baked than conventionally baked pound cake. RS3 increased significantly in conventionally baked products stored for 8 days at room temperature, whereas slightly lower changes in RS3 were observed in the microwaved product. DSC revealed less gelatinisation in microwaved pound cake which is related to limited water availability during the microwave heating process. The crystallinity peaks present in conventionally baked pound cake might be associated with RS3 content; the resistant retrograded starch formed during storage, is reflected in the XRD pattern.

CONCLUSION: Microwave‐baked pound cake crumbs showed less gelatinisation than conventionally baked pound cake crumbs. Copyright © 2007 Society of Chemical Industry
Phosphorus status on Canadian organic farms
Authors: Martin Ralph C , Lynch Derek H , Frick Brenda , van Straaten Peter
Published: September 2007

In eastern North America, many conventional livestock farms, especially dairy farms with high inputs of feed and fertiliser have excess soil phosphorus levels and an annual phosphorus surplus. However, a Canadian dairy farm in transition to organic, without fertiliser inputs reduced its farm P surplus to a marginal level. On long‐term organic dairy farms in Ontario, most soils tested low to very low in available P as measured by a standard soil test. Canadian Prairie organic grain farms also consistently demonstrate deficiencies in available soil P. Organic producers have few viable alternatives for P management. Phosphate rock can be acceptable to organic standards (provided they are low in heavy metals, and not processed synthetically), but the P in these becomes available slowly, especially in high pH soils common on most organic farms in Canada. An alternative is to increase soil P availability. Enhanced microbial activity in organically managed soils may make P more available. Livestock manures are rich sources of available phosphorus, but a majority of organic farmers in Canada do not keep livestock. Off‐farm manure sources are subject to organic regulations and hauling costs, both of which may be prohibitive. Furthermore, manure from conventional farms in Canada may be contaminated by genetically modified material from corn and soybean feed. Additional research is required to improve short‐term availability of soil P and long‐term replacement. Copyright © 2007 Society of Chemical Industry
Proton‐Conducting Zirconium Pyrophosphate/Poly(2,5‐benzimidazole) Composite Membranes Prepared by a PPA Direct Casting Method
Authors: Kim Tae‐Ho , Lim Tae‐Wook , Park Yong‐Su , Shin Kyusoon , Lee Jong‐Chan
Published: September 2007

Zirconium pyrophosphate (ZPP)/poly(2,5‐benzimidazole) composites were prepared by polymerization of 3,4‐diaminobenzoic acid with zirconium hydrogen phosphate in polyphosphoric acid. The composite membranes for polymer electrolyte membranes were prepared by casting the polymerization solutions directly onto stainless steel plates. Membranes doped in 60 wt.‐% phosphoric acid solution had high proton conductivity values of more than 0.12 S · cm−1 (at 180 °C and 1% RH). Physical properties of the doped membranes, including the mechanical strength and dimensional stability, improved as ZPP content in the composites increased to 10–20 wt.‐%.

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Random Networks, Graphs, and Matrices
Authors: Eichinger B. E.
Published: September 2007

Summary: The theory of elasticity based on the distribution function of the gyration tensor is reviewed. It is shown that the James‐Guth potential for a network is a model potential of mean force, derivable in principle from the true many‐body potential for the elastic body. The determination of the modulus of elasticity is resolved in the calculation of the statistical mechanical average of the smallest, non‐zero, eigenvalue of the connectivity matrix that describes the network. The mathematical problem to determine the spectrum of eigenvalues of the random network can be couched in both the language of random graphs and of random matrices.
Toughness Properties of Lightly Crosslinked Epoxies Using Block Copolymers
Authors: Gerard Pierre , Boupat Nicolas Passade , Fine Thomas , Gervat Laurent , Pascault Jean‐Pierre
Published: September 2007

Summary: In this work is discussed an alternative approach to the toughening of epoxy networks by the addition of acrylic block copolymers, composed of rigid and rubbery blocks. Once the reaction is completed, the initial self‐assembly of block copolymers in epoxy thermoset precursors produces rubbery domains: depending on the block copolymer structure and composition, these domains are of the micrometer or the nanometer size. Nanostructures are obtained when the rigid block is a random copolymer of methylmethacrylate and N,N‐dimethylacrylamide. The rubbery domains prevent rapid crack propagation and the highest toughness is obtained with filament‐like microparticles or wormlike micelles.
X‐ray Photon Correlation Spectroscopy of Dynamics in Thermosensitive Gels
Authors: Geissler Erik , Kosik Katalin , Fluerasu Andrei , Moussaïd Abdellatif , László Krisztina
Published: September 2007

Summary: Temperature‐sensitive hydrogels undergo a volume phase transition (VPT) when heated above a critical temperature Tc. For the poly(N‐isopropyl acrylamide) (PNIPA)‐water system, Tc. = 34 °C. Below Tc the gels are transparent and highly swollen. On warming above Tc they promptly turn white and start to deswell. The rate of deswelling, however, can be orders of magnitude slower than that of swelling below Tc. The unstable intermediate structure above Tc, can retain the solvent and conserve the sample volume for may days, even with millimetre‐sized samples.

Light scattering observations of the internal structure of these gels above Tc are precluded by their strong turbidity. Small angle X‐ray scattering measurements (SAXS), on the other hand, are less subject to multiple scattering as X‐rays penetrate more easily into the bulk material. Conventional (incoherent) SAXS observations reveal intense scattering from smooth internal water‐polymer interfaces with an estimated surface area of about 7 m2/g in the swollen gel. The dynamics in the off‐equilibrium high temperature state, investigated by X‐ray photon correlation spectroscopy (XPCS), displays a relaxation rate that is linearly proportional to the wavevector q, rather than to q2 as in diffusion processes. The physical origin of this relaxation is consistent with jamming, a phenomenon that is common in other disordered systems.
Polymethacrylate Networks as Substrates for Cell Culture
Authors: Sun Y. , Maughan J. , Haigh R. , Hopkins S. A. , Wyman P. , Johnson C. , Fullwood N. J. , Ebdon J. , MacNeil S. , Rimmer S.
Published: September 2007

Summary: methacrylate networks have a long history of applications in medical technology and much is known of their non‐fouling properties. However, in recent times it has become clear that the swollen nature of these materials may provide some advantages if they are used as scaffolds in tissue engineering. In general however these hydrogels are resistant to protein adsorption and human cells do not easily adhere. In this work we provide an overview of several strategies that are designed to improve the cell‐adhesive properties of hydrogels while maintaining their useful properties, mainly ease of diffusion of nutrients and growth factors. We describe our early attempts at modifying hydrogels based on 2,3‐propandiol ‐1‐methacrylate, with either hydrophobic units or acid groups. Modification with lauryl methacrylate produced an improvement but acid modification failed to provide surfaces that were conducive to cell culture. Much better scaffolds were prepared by amination of epoxy functional 2,3‐propandiol‐1‐methacrylate networks. Optimized materials in this class were shown to be good substrates for the co‐culture of bovine keratocytes with human corneal epithelial cells. We also describe the synthesis and biological properties of methacrylate conetworks, which phase separate during synthesis to give porous amphiphilic materials. Optimization of these materials produces materials that perform as well as tissue culture plastic so that confluent sheets of human dermal fibroblasts can be produced using standard culture techniques.
Molecular Weight Influence on Gelatin Gels: Structure, Enthalpy and Rheology
Authors: Elharfaoui Nadia , Djabourov Madeleine , Babel Wilfried
Published: September 2007

Summary: This paper deals with the gelation properties of gelatins with various molecular weights. The samples are 4 different extracts from limed bones. We investigated firstly the structural properties: the helix amounts by optical rotation measurements and the enthalpy of helix formation and melting, with the same thermal protocols and for various concentrations. Comparison between the two methods allowed deriving the enthalpy of helix‐coil transition and melting. Rheology was performed under the same conditions with a stress controlled rheometer working with a fixed, very small, strain during gel formation, maturation and melting. Correlation between all the measurements confirms the existence of the master curve for storage modulus versus gelatin concentration for all samples investigated.
Synthesis and Viscoelastic Properties of Hydrophobically Modified Hydrogels
Authors: Miquelard‐Garnier Guillaume , Creton Costantino , Hourdet Dominique
Published: September 2007

Summary: We report the synthesis and characterization of a family of hydrophobically modified hydrogels designed to have an improved fracture resistance. A backbone of poly(acrylic acid) (PAA) was functionalized with double bonds and hydrophobic groups. The functionalized PAA was then crosslinked with a dithiol. The chemical structure of the gels was characterized with a combination of NMR, titration methods and rheological techniques. The crosslinked structure of the hydrogel was found to be dependent on the polymer concentration only, while the dissipative properties of the gel increased strongly at all frequencies, with the introduction of hydrophobic groups which formed reversible associations. We expect these viscoelastic hydrogels to display dramatically different properties from the unmodified hydrogels when stretched and fractured.
Parkinson's disease and resistive exercise: Rationale, review, and recommendations
Authors: Falvo Michael J. , Schilling Brian K. , Earhart Gammon M.
Published: September 2007

Individuals with Parkinson's disease (PD) are not only burdened with disease‐specific symptoms (i.e., bradykinesia, rigidity, and tremor), but are also confronted with age‐associated progressive loss of physical function, perhaps to a greater extent than neurologically normal adults. Suggestions for the inclusion of resistive exercise into treatment to attenuate these symptoms were made over 10 years ago, yet very few well controlled investigations are available. The objective of this review is to establish a clear rationale for the efficacy of resistance training in individuals with PD. Specifically, we highlight musculoskeletal weakness and its relationship to function as well as potential training‐induced adaptive alterations in the neuromuscular system. We also review the few resistance training interventions currently available, but limit this review to those investigations that provide a quantitative exercise prescription. Finally, we recommend future lines of inquiry warranting further attention and call to question the rationale behind current exercise prescriptions. The absence of reports contraindicating resistive exercise, the potential for positive adaptation, and the noted benefits of resistance training in other populations may provide support for its inclusion into a treatment approach to PD. © 2007 Movement Disorder Society
Delayed‐onset dystonia due to perinatal asphyxia: A prospective study
Authors: Nataša Cerovac  , Petrović Igor , Klein Christine , Kostić Vladimir S.
Published: September 2007

The objective of this work was to establish the existence and incidence of possible delayed‐onset dystonia in a cohort of infants with diagnosed perinatal asphyxial hypoxic‐ischemic encephalopathy (HIE). This prospective study comprised 103 survivors of perinatal asphyxial HIE, who were regularly followed and neurologically examined in the course of 7 to 13 years after birth (median 10 years). Neurological outcome at the end of the follow‐up period was normal in 87 (84.5%) patients, while in 7 (6.8%) only mild neurological signs were detected (behavioral disturbances in 3, clumsiness in 2, and hypotonia in 1 patient). Severe cerebral palsy was diagnosed in nine patients (8.7%). Only one patient was diagnosed with possible delayed‐onset segmental dystonia. At the age of 4 years he developed cervical dystonia with spread to one arm in the course of 1.5 years (segmental dystonia) and then stabilized. Other known causes of dystonia, including a DYT1 mutation, were excluded. Our preliminary data suggest that over the course of at least 7 years after birth, approximately 1% of infants who survived perinatal asphyxial HIE would develop delayed‐onset dystonia. © 2007 Movement Disorder Society
Switching costs, dynamic uncertainty, and buyer–seller relationships
Authors: Murthy Nagesh N. , Shrikhande Milind , Subramanian Ajay
Published: September 2007

We analyze strategic relationships between buyers and sellers in markets with switching costs and dynamic uncertainty by investigating the scenario wherein a representative buyer trades with two foreign sellers located in the same foreign country. We show that, under exchange rate uncertainty, switching costs may lead to switching equilibria where both sellers co‐exist in the market with the buyer, or no‐switching equilibria where either seller captures the market. The presence of exchange rate uncertainty facilitates competition by allowing the sellers to co‐exist in the market with the buyer. However, if the level of uncertainty is beyond a threshold, the only viable equilibria are those where one of the sellers captures the market. Further, depending on the level of exchange rate uncertainty and the sellers' variable costs, switching costs may either raise or lower the level of prices in long‐term contracts between the buyer and the sellers. © 2007 Wiley Periodicals, Inc. Naval Research Logistics, 2007
Synthesis of an α‐amino nitrile and a bis α‐amino nitrile derivative of thiadiazole: reaction mechanism
Authors: Mirífico María Virginia , Caram José Alberto , Piro Oscar Enrique , Vasini Enrique Julio
Published: September 2007

The first nucleophilic addition of an inorganic nucleophile (cyanide) to the activated, rigid, α‐diazomethine groups of a 1,2,5‐thiadiazole 1,1‐dioxide is reported here. An α‐amino nitrile and a bis α‐amino nitrile derivatives were obtained in good yields (62 and 98%, respectively) and characterized by spectroscopic, analytical, and single crystal X‐ray diffraction techniques. The course of the reaction, followed by cyclic voltammetry (CV), showed that cyanide adds to only one of the two CN double bonds of the thiadiazole, forming an anion from which an N‐methyl derivative was obtained. Adequate concentrations of cyanide and methyl iodide (MeI) produced directly the bis α‐amino nitrile derivative. Copyright © 2007 John Wiley & Sons, Ltd.
A diverse view of protein dynamics from NMR studies of HIV‐1 protease flaps
Authors: Ishima Rieko , Louis John M.
Published: September 2007

Internal motion in proteins fulfills a multitude of roles in biological processes. NMR spectroscopy has been applied to elucidate protein dynamics at the atomic level, albeit at a low resolution, and is often complemented by molecular dynamics simulation. However, it is critical to justify the consistency between simulation results and conclusions often drawn from multiple experiments in which uncertainties arising from assumed motional models may not be explicitly evaluated. To understand the role of the flaps of HIV‐1 protease dimer in substrate recognition and protease function, many molecular dynamics simulations have been performed. The simulations have resulted in various proposed models of the flap dynamics, some of which are more consistent than others with our working model previously derived from experiments. However, using the working model to discriminate among the simulation results is not straightforward because the working model was derived from a combination of NMR experiments and crystal structure data. In this study, we use the NMR chemical shifts and relaxation data of the protease “monomer” rather than structural data to narrow down the possible conformations of the flaps of the “dimer”. For the first time, we show that the tips of the flaps in the unliganded protease dimer interact with each other in solution. Accordingly, we discuss the consistency of the simulations with the model derived from all experimental data. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Local structure of interstitial Zn in β‐Zn4Sb3
Authors: Toberer E. S. , Sasaki K. A. , Chisholm C. R. I. , Haile S. M. , Goddard W. A. , Snyder G. J.
Published: September 2007

The low thermal conductivity of the thermoelectric material β‐Zn4Sb3 has been linked to disorder arising from multiple interstitial Zn sites. Here we investigate the energetics and local distortions associated with these interstitial sites via DFT calculations. Our results show the β‐Zn4Sb3 structure is able to distort into many inequivalent geometries of similar energies, suggesting a topology rich with transport pathways through energetically accessible metastable states. The occurrence of such a shallow energy landscape may explain the recently discovered liquid‐like diffusivity of Zn in β‐Zn4Sb3 – comparable to that found in superionic conductors. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Examining the collision‐induced decomposition spectra of ammoniated triglycerides. III. The linoleate and arachidonate series
Authors: Gakwaya Robert , Li Xingwen , Wong Yin Ling , Chivukula Swathilekha , Collins Elizabeth J. , Evans Jason J.
Published: September 2007

A series of positionally pure triglycerides (TAGs) of the form LXL, YLY, AXA, and YAY was synthesized and analyzed by reversed‐phase high‐performance liquid chromatography/tandem mass spectrometry. L and A represent the linoleate and arachidate moieties, respectively, and X and Y represent large arrays of fatty acid moieties of various chain lengths, degree of unsaturations, double‐bond positions, and cis/trans configurations. The abundances of the collision‐induced decomposition (CID) products of ammoniated TAGs were examined as a function of these parameters. The major CID products, the diglyceride (DAG) product ions and the MH+ ions, are plotted as functions of chain length for the saturated and monounsaturated series of X and Y. The following trends are observed in the data. TAGs with higher degrees of unsaturation tend to show greater relative abundances of MH+ in the CID spectra of their ammoniated precursor ions. The position of the fatty acid constituents along the glycerol backbone also seems to influence the abundances of the MH+ ion in the CID spectra of the ammoniated precursor ions. A fatty acid constituent with double bonds along the fatty acid chain positioned close to the carbonyl promotes the formation of the DAG product ion that corresponds to its loss upon CID of the ammoniated precursor ion. Linoleic acid substituents also seem to promote the formation of DAG product ions, but to a lesser extent. Data for the YAY TAGs are used to predict the abundances of the product ions in the CID spectra of ammoniated YAX TAGs. These data are discussed in context of a broader project to develop and validate software algorithims to support a platform for comprehensive analysis of complex mixtures of TAGs. Copyright © 2007 John Wiley & Sons, Ltd.
Partial Splenectomy for Benign Splenic Cysts with the Aid of a Lin Clamp: Technical Note
Authors: Wu Shih‐Chung , Wang Chih‐Chi , Yong Chee‐Chien
Published: September 2007

Background

Spleen‐preserving procedures deserve every effort by surgeons to reduce the risk of overwhelming postsplenectomy infection. Partial splenectomy at hospitals with restricted sources remains technically demanding. We describe our method of partial splenectomy for benign splenic cysts with the aid of a Lin clamp.

Patients and Methods

Since April 2003 to August 2004, we have performed partial splenectomy with the aid of a Lin clamp on 5 suitable patients with symptomatic cysts. Detailed patient characteristics, operative variables, and outcomes were collected. Following surgery, they were regularly followed up every 6 months.

Results

All five partial splenectomies were successfully executed without any complications. The mean operating time was 75 minutes, and a mean operative blood loss of 68 ml could be achieved. With a mean follow‐up of 34.4 months, no cyst recurrences were detected to date. Postoperative laboratory data, imaging studies, and clinical situations proved that the preserved splenic parenchyma maintained adequate function.

Conclusions

Partial splenectomy with the aid of a Lin clamp for benign splenic cysts is a practical method with the advantages of easy application, rapid parenchymal dissection, secure hemostasis, and cost‐effectiveness. With encouraging preliminary results, further application of this method to bleeding eccentric parenchymal injuries of the spleen may be warranted.
Efficacy and Safety of Seprafilm for Preventing Postoperative Abdominal Adhesion: Systematic Review and Meta‐analysis
Authors: Zeng Qiqiang , Yu Zhengping , You Jie , Zhang Qiyu
Published: September 2007

Background

There is no clear consensus on the efficacy and safety of hyaluronate‐carboxymethylcellulose membrane (Seprafilm) for preventing postoperative abdominal adhesion. This study is a meta‐analysis of the available evidence.

Methods

A search of the MEDLINE, EMBASE, and the Cochrane Library identified eight studies that met the inclusion criteria for data extraction. Estimates of effectiveness were performed using fixed‐ and random‐effects models. The effect was calculated as an odds ratio (OR) with 95% confidence intervals (CI) using the statistical software Review Manager Version 4.2. Level of significance was set at p < 0.05.

Results

Outcomes of 4203 patients were studied. The incidence of grade 0 adhesions among Seprafilm‐treated patients was statistically significantly more than that observed among control group patients (OR 95%CI, 3.74–20.34; p < 0.01). There was no significant difference in the incidence of grade 1 adhesions between Seprafilm and control groups (OR 95%CI, 0.58–2.71; p = 0.56). The severity of grade 2 and grade 3 adhesions among Seprafilm‐treated patients was significantly less than that observed among control group patients (OR 95%CI, 0.22–0.93; p = 0.03; OR 95%CI, 0.09–0.63; p < 0.01, respectively). The incidence of intestinal obstruction after abdominal surgery was not different between Seprafilm and control groups (OR 95%CI, 0.78–1.23; p = 0.84). Using Seprafilm significantly increased the incidence of abdominal abscesses (OR 95%CI, 1.06–2.54; p = 0.03) and anastomotic leaks (OR 95%CI, 1.18–3.50; p = 0.01).

Conclusions

Our systematic review and meta‐analysis showed that Seprafilm could decrease abdominal adhesions after general surgery, which may benefit patients, but could not reduce postoperative intestinal obstruction. At the same time, Seprafilm did increase abdominal abscesses and anastomotic leaks.
HighP–T Nano-Mechanics of Polycrystalline Nickel
Authors: Zhao Yusheng , Shen TD , Zhang Jianzhong
Published: September 2007

We have conducted highP–T synchrotron X-ray and time-of-flight neutron diffraction experiments as well as indentation measurements to study equation of state, constitutive properties, and hardness of nanocrystalline and bulk nickel. Our lattice volume–pressure data present a clear evidence of elastic softening in nanocrystalline Ni as compared with the bulk nickel. We show that the enhanced overall compressibility of nanocrystalline Ni is a consequence of the higher compressibility of the surface shell of Ni nanocrystals, which supports the results of molecular dynamics simulation and a generalized model of a nanocrystal with expanded surface layer. The analytical methods we developed based on the peak-profile of diffraction data allow us to identify “micro/local” yield due to high stress concentration at the grain-to-grain contacts and “macro/bulk” yield due to deviatoric stress over the entire sample. The graphic approach of our strain/stress analyses can also reveal the corresponding yield strength, grain crushing/growth, work hardening/softening, and thermal relaxation under highP–T conditions, as well as the intrinsic residual/surface strains in the polycrystalline bulks. From micro-indentation measurements, we found that a low-temperature annealing (T < 0.4 Tm) hardens nanocrystalline Ni, leading to an inverse Hall–Petch relationship. We explain this abnormal Hall–Petch effect in terms of impurity segregation to the grain boundaries of the nanocrystalline Ni.
Letrozole as primary therapy for endometrial hyperplasia in young women
Authors: Li Hongzhen , Chen Xinna , Qiao Jie
Published: September 2007

Objective

To study letrozole as a primary therapeutic agent for endometrial hyperplasia with or without atypia in young women.

Methods

Five premenopausal women presenting for infertility were diagnosed as having endometrial hyperplasia. A second biopsy was performed after they were treated for 3 months with 2.5 mg of letrozole per day. Serum levels of estradiol and progesterone were measured each month.

Results

Curettage of the endometrium at the end of treatment revealed no evidence of endometrial hyperplasia or atypia in any of the patients. Low serum levels of estradiol were found in all patients.

Conclusion

This case series indicates that aromatase inhibitors deserve attention for the conservative treatment of endometrial hyperplasia. However, more studies are needed to confirm the efficacy and safety of this agent.
Achieving transparency in implementing abortion laws
Authors: Cook R.J. , Erdman J.N. , Dickens B.M.
Published: September 2007

National and international courts and tribunals are increasingly ruling that although states may aim to deter unlawful abortion by criminal penalties, they bear a parallel duty to inform physicians and patients of when abortion is lawful. The fear is that women are unjustly denied safe medical procedures to which they are legally entitled, because without such information physicians are deterred from involvement. With particular attention to the European Court of Human Rights, the UN Human Rights Committee, the Constitutional Court of Colombia, the Northern Ireland Court of Appeal, and the US Supreme Court, decisions are explained that show the responsibility of states to make rights to legal abortion transparent. Litigants are persuading judges to apply rights to reproductive health and human rights to require states’ explanations of when abortion is lawful, and governments are increasingly inspired to publicize regulations or guidelines on when abortion will attract neither police nor prosecutors’ scrutiny.
Evidence‐based medicine and otolaryngology–HNS: Passing fashion or permanent solution
Authors: Burton Martin J.
Published: September 2007

Otolaryngologists and head and neck surgeons have not always fully engaged with the evidence‐based medicine (EBM) movement. Now that EBM has been identified as one of the most important milestones in medicine in the last 150 years, I hope things will change. In reviewing the tenets of EBM and considering its implementation I explain why we must embrace its principles and argue that optimal medical practice is both “evidence” – and “wisdom”‐based, both being necessary but neither alone being sufficient.
Proteomics Technologies and Challenges
Authors: Cho William C.S.
Published: September 2007

Proteomics is the study of proteins and their interactions in a cell. With the completion of the Human Genome Project, the emphasis is shifting to the protein compliment of the human organism. Because proteome reflects more accurately on the dynamic state of a cell, tissue, or organism, much is expected from proteomics to yield better disease markers for diagnosis and therapy monitoring. The advent of proteomics technologies for global detection and quantitation of proteins creates new opportunities and challenges for those seeking to gain greater understanding of diseases. High-throughput proteomics technologies combining with advanced bioinformatics are extensively used to identify molecular signatures of diseases based on protein pathways and signaling cascades. Mass spectrometry plays a vital role in proteomics and has become an indispensable tool for molecular and cellular biology. While the potential is great, many challenges and issues remain to be solved, such as mining low abundant proteins and integration of proteomics with genomics and metabolomics data. Nevertheless, proteomics is the foundation for constructing and extracting useful knowledge to biomedical research. In this review, a snapshot of contemporary issues in proteomics technologies is discussed.
Integration of Known Transcription Factor Binding Site Information and Gene Expression Data to Advance from Co-Expression to Co-Regulation
Authors: Clements Maarten , van Someren Eugene P. , Knijnenburg Theo A. , Reinders Marcel J.T.
Published: September 2007

The common approach to find co-regulated genes is to cluster genes based on gene expression. However, due to the limited information present in any dataset, genes in the same cluster might be co-expressed but not necessarily co-regulated. In this paper, we propose to integrate known transcription factor binding site information and gene expression data into a single clustering scheme. This scheme will find clusters of co-regulated genes that are not only expressed similarly under the measured conditions, but also share a regulatory structure that may explain their common regulation. We demonstrate the utility of this approach on a microarray dataset of yeast grown under different nutrient and oxygen limitations. Our integrated clustering method not only unravels many regulatory modules that are consistent with current biological knowledge, but also provides a more profound understanding of the underlying process. The added value of our approach, compared with the clustering solely based on gene expression, is its ability to uncover clusters of genes that are involved in more specific biological processes and are evidently regulated by a set of transcription factors.
Adaptive Evolution of Cry Genes in Bacillus Thuringiensis: Implications for Their Specificity Determination
Authors: Wu Jin-Yu , Zhao Fang-Qing , Bai Jie , Deng Gang , Qin Song , Bao Qi-Yu
Published: September 2007

The cry gene family, produced during the late exponential phase of growth in Bacillus thuringiensis, is a large, still-growing family of homologous genes, in which each gene encodes a protein with strong specific activity against only one or a few insect species. Extensive studies are mostly focusing on the structural and functional relationships of Cry proteins, and have revealed several residues or domains that are important for the target recognition and receptor attachment. In this study, we have employed a maximum likelihood method to detect evidence of adaptive evolution in Cry proteins, and have identified 24 positively selected residues, which are all located in Domain II or III. Combined with known data from mutagenesis studies, the majority of these residues, at the molecular level, contribute much to the insect specificity determination. We postulate that the potential pressures driving the diversification of Cry proteins may be in an attempt to adapt for the “arm race” between δ-endotoxins and the targeted insects, or to enlarge their target spectra, hence result in the functional divergence. The sites identified to be under positive selection would provide targets for further structural and functional analyses on Cry proteins.
Dynamic Proteome Changes of Shigella Flexneri 2a During Transition from Exponential Growth to Stationary Phase
Authors: Zhu Li , Liu Xian-Kai , Zhao Ge , Zhi Yi-Dan , Bu Xin , Ying Tian-Yi , Feng Er-Ling , Wang Jie , Zhang Xue-Min , Huang Pei-Tang , Wang Heng-Liang
Published: September 2007

Shigella flexneri is an infectious pathogen that causes dysentery to human, which remains a serious threat to public health, particularly in developing countries. In this study, the global protein expression patterns of S. flexneri during transition from exponential growth to stationary phase in vitro were analyzed by using 2-D PAGE combined with MALDI-TOF MS. In a time-course experiment with five time points, the relative abundance of 49 protein spots varied significantly. Interestingly, a putative outer membrane protein YciD (OmpW) was almost not detected in the exponential growth phase but became one of the most abundant proteins in the whole stationary-phase proteome. Some proteins regulated by the global regulator FNR were also significantly induced (such as AnsB, AspA, FrdAB, and KatG) or repressed (such as AceEF, OmpX, SodA, and SucAB) during the growth phase transition. These proteins may be the key effectors of the bacterial cell cycle or play important roles in the cellular maintenance and stress responses. Our expression profile data provide valuable information for the study of bacterial physiology and form the basis for future proteomic analyses of this pathogen.
FragAnchor: A Large-Scale Predictor of Glycosylphosphatidylinositol Anchors in Eukaryote Protein Sequences by Qualitative Scoring
Authors: Poisson Guylaine , Chauve Cedric , Chen Xin , Bergeron Anne
Published: September 2007

A glycosylphosphatidylinositol (GPI) anchor is a common but complex C-terminal post-translational modification of extracellular proteins in eukaryotes. Here we investigate the problem of correctly annotating GPI-anchored proteins for the growing number of sequences in public databases. We developed a computational system, called FragAnchor, based on the tandem use of a neural network (NN) and a hidden Markov model (HMM). Firstly, NN selects potential GPI-anchored proteins in a dataset, then HMM parses these potential GPI signals and refines the prediction by qualitative scoring. FragAnchor correctly predicted 91% of all the GPI-anchored proteins annotated in the Swiss-Prot database. In a large-scale analysis of 29 eukaryote proteomes, FragAnchor predicted that the percentage of highly probable GPI-anchored proteins is between 0.21% and 2.01%. The distinctive feature of FragAnchor, compared with other systems, is that it targets only the C-terminus of a protein, making it less sensitive to the background noise found in databases and possible incomplete protein sequences. Moreover, FragAnchor can be used to predict GPI-anchored proteins in all eukaryotes. Finally, by using qualitative scoring, the predictions combine both sensitivity and information content. The predictor is publicly available at http://navet.ics.hawaii.edu/~fraganchor/NNHMM/NNHMM.html.