bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electronic structures of heme a of cytochrome c oxidase in the redox states—Charge density migration to the propionate groups of heme a
Authors: Takano Yu , Nakamura Haruki 
Published: July 2009

AbstractThe electronic structures of heme a of cytochrome c oxidase in the redox states were studied, using hybrid density functional theory with a polarizable continuum model and a point charge model. We found that the most stable electronic configurations of the d electrons of the Fe ion are determined by the orbital interactions of the d orbitals of the Fe ion with the π orbitals of the porphyrin ring and the His residues. The redox reaction of the Fe ion influences the charge density on the formyl group through the π conjugation of the porphyrin ring. In addition, we found the charge transfer from the Fe ion to the propionate group of heme a in the redox change despite the lack of the π‐conjugation. We elucidated that the charge propagation originates from the heme a structure itself and that the origin of the charge delocalization to the heme propionate is the orbital interactions between the d orbital of the Fe ion and the p orbitals of the carboxylate part of the heme propionate via the π conjugation of the porphyrin ring and the σ* orbital of the CC bond of the propionate group. The electrostatic effect by surrounding proteins enhances the charge transfer from the Fe ion to the propionate group. These results indicate that heme propionate groups serve electron mediators in electron transfer as well as electrostatic anchors, and that proteins surrounding the active site reinforce the congenital abilities of the cofactors. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010
Methods for calculating the absolute entropy and free energy of biological systems based on ideas from polymer physics
Authors: Meirovitch Hagai 
Published: July 2009

AbstractThe commonly used simulation techniques, Metropolis Monte Carlo (MC) and molecular dynamics (MD) are of a dynamical type which enables one to sample system configurations i correctly with the Boltzmann probability, P, while the value of P is not provided directly; therefore, it is difficult to obtain the absolute entropy, S ∼ −ln P, and the Helmholtz free energy, F. With a different simulation approach developed in polymer physics, a chain is grown step‐by‐step with transition probabilities (TPs), and thus their product is the value of the construction probability; therefore, the entropy is known. Because all exact simulation methods are equivalent, i.e. they lead to the same averages and fluctuations of physical properties, one can treat an MC or MD sample as if its members have rather been generated step‐by‐step. Thus, each configuration i of the sample can be reconstructed (from nothing) by calculating the TPs with which it could have been constructed. This idea applies also to bulk systems such as fluids or magnets. This approach has led earlier to the “local states” (LS) and the “hypothetical scanning” (HS) methods, which are approximate in nature. A recent development is the hypothetical scanning Monte Carlo (HSMC) (or molecular dynamics, HSMD) method which is based on stochastic TPs where all interactions are taken into account. In this respect, HSMC(D) can be viewed as exact and the only approximation involved is due to insufficient MC(MD) sampling for calculating the TPs. The validity of HSMC has been established by applying it first to liquid argon, TIP3P water, self‐avoiding walks (SAW), and polyglycine models, where the results for F were found to agree with those obtained by other methods. Subsequently, HSMD was applied to mobile loops of the enzymes porcine pancreatic α‐amylase and acetylcholineesterase in explicit water, where the difference in F between the bound and free states of the loop was calculated. Currently, HSMD is being extended for calculating the absolute and relative free energies of ligand–enzyme binding. We describe the whole approach and discuss future directions. Copyright © 2009 John Wiley & Sons, Ltd.
Synthesis, molecular structure, IR and Raman spectra as well as DFT chemical calculations for alkylamides of thiocyanoacetic acid
Authors: Kucharska E. , Lorenc J. , Sa̧siadek W. , Ban‐Oganowska H. , Talik Z. , Hanuza J. , Ma̧czka M. 
Published: July 2009

AbstractThis paper reports on room‐temperature infrared (IR) and Raman studies and vibrational characteristics of amide and thiocyano groups of R‐NH‐CO‐CH2‐SCN n‐alkylamides of thiocyanoacetic acid (R = C8H17, C9H19, C12H25 and C14H29). Their molecular structure has been proposed on the basis of optimization process. The experimental wavenumbers have been compared to those obtained from discrete Fourier transform (DFT) quantum chemical calculations performed with the use of B3LYP/6–31G(d,p) approximation. The role of the hydrogen bonds in the stabilization of the structure has been analyzed. It was found that the hydrogen bonding and strong dynamic interactions between the unit cell components are responsible for the deviation of several theoretical wavenumbers from the experimental ones. Copyright © 2009 John Wiley & Sons, Ltd.
Optimising tip‐enhanced optical microscopy
Authors: Downes Andrew , Mouras Rabah , Mari Meropi , Elfick Alistair 
Published: July 2009

AbstractWe discuss the range of tip‐enhanced optical microscopies—namely mapping scattered light, fluorescence, Raman and coherent anti‐Stokes Raman scattering (CARS) signals on the scale of 10–20 nm. Through the use of measurements and finite‐element simulations, we explain what the optimum tip materials and sizes are and illumination wavelengths to use for all these modes of imaging. We also show that the observed limit of 50–100 µW of illumination power is due to a temperature rise of tens of degrees beneath the tip apex, and is most likely linked to the evaporation of water from the tip apex region. This has two important implications—that the tip is surrounded by water even when imaging ‘in air’, and that the tip and sample are both heated when imaging. With emphasis on Raman and CARS, we discuss how both these types of tip‐enhanced optical microscopy can be made about as fast as their diffraction‐limited counterparts. Copyright © 2009 Her Majesty the Queen in right of Canada. Published by John Wiley & Sons. Ltd.
The minor salivary gland biopsy as a diagnostic tool for Sjogren syndrome
Authors: Bamba Ravinder , Sweiss Nadera J. , Langerman Alexander J. , Taxy Jerome B. , Blair Elizabeth A. 
Published: July 2009

AbstractObjectives/Hypothesis:In suspected cases of Sjogren syndome (SS), patients are often referred for a labial minor salivary gland biopsy. However, studies have shown this test to be unreliable. Pathologic misinterpretation and immunosuppressive medications may affect the results of the biopsy. As a result, it is best to perform this procedure only when necessary. The purpose of the current study was to review clinical signs and symptoms of patients who underwent a lip biopsy to determine which patients benefited most from this procedure.Study Design:Retrospective review.Methods:A retrospective chart review of patients referred to otolaryngology for a lip biopsy for the diagnosis of SS.Results:Joint pain, salivary gland swelling, and abnormal serology (anti‐Sjogren syndrome A/anti‐Sjogren syndrome B) were more prevalent in the positive lip biopsy group (grade = 3 or 4). Out of the 12 patients who had both sicca symptoms and positive serology, nine (75%) had a grade = 4. Presence of sicca symptoms and positive serology were predictive of a positive biopsy (P = .017). Excluding those patients who were on immunosuppression for more than 6 weeks prior to the biopsy, the correlation became stronger (P = .011).Conclusions:In this study, clinical presentation of sicca symptoms and positive serology reliably predicted the results of a lip biopsy. The results of this study suggest that patients with clear criterion for SS may not require a lip biopsy, especially those patients on immunosuppression. When physicians suspect SS, a thorough clinical and laboratory examination is necessary to determine if a patient will benefit from a minor salivary gland biopsy. Laryngoscope, 2009
Cochlear nerve diameter in normal hearing ears using high‐resolution magnetic resonance imaging
Authors: Jaryszak Eric M. , Patel Nimish A. , Camp Morgan , Mancuso Anthony A. , Antonelli Patrick J. 
Published: July 2009

AbstractObjectives:Deficient cochlear nerves (CN) have been associated with poor cochlear implant performance. Normative data on CN diameter based on radiographic imaging have not been published. The objectives of this study were to determine if CN diameter could be reproducibly measured on parasagittal constructive interference in steady state (CISS)‐sequence magnetic resonance imaging (MRI) and to establish a normative range for CN diameter.Study Design:Retrospective review of MRI images by two independent blinded observers.Methods:Thirty patients (45 ears) with a CISS‐sequence MRI done for auditory complaints in patients with normal hearing in one ear were included. CN diameters were measured in a parasagittal plane just medial to the internal auditory canal (IAC) fundus by two independent observers. Cross‐sectional areas were calculated and interobserver agreement was evaluated.Results:The CN was identified in 100% of studied ears. In 93%, the diameters were able to be measured by both observers. In 7% of ears, the cochlear nerve was unable to be measured secondary to the proximity of the CN to IAC wall. The CN vertical diameter (1.4 mm ± 0.21 mm), horizontal diameter (1.0 mm ± 0.15 mm), and cross‐sectional area (1.1 mm ± 0.26 mm2) were normally distributed. There was good interobserver correlation for each measure.Conclusions:CN diameter can be reliably measured at the IAC fundus. This study establishes normative radiographic data for the CN diameter. These data may be used to evaluate the cause and treatment prognosis in patients with sensorineural hearing loss. Laryngoscope, 2009
Acellular dermis compared to skin grafts in oral cavity reconstruction
Authors: Girod Douglas A. , Sykes Kevin , Jorgensen Jeffery , Tawfik Ossama , Tsue Terance 
Published: July 2009

AbstractObjectives/Hypothesis:To compare the efficacy of acellular dermal matrix (ADM) and split thickness skin grafts (STSG) in oral cavity reconstruction.Study Design:Prospective cohort study.Methods:Thirty‐four patients were included in this study (ADM, n = 22; STSG, n = 12). Evaluation for patient demographics, graft site, graft contracture, and functional status as defined by the EORTC QLQ‐C30 and the H&N35 questionnaires. A subgroup of patients underwent graft site biopsy for histological analysis. A cost estimate of both procedures was also performed.Results:Patient groups were similar in age, sex, race, smoking exposure, and site grafted. More patients were treated with radiation therapy (pre‐ or postoperative) in the ADM group (45%) compared to the STSG group (17%). Graft failure rate was higher in the ADM group (14% vs. 0%), and both groups had similar estimated graft contraction. The quality of life survey results favored the ADM group, but only the category of trouble with social eating was statistically significant (P= .03). Radiation therapy had a significantly negative impact for both ADM and STSG. Histology demonstrated increased inflammation, fibrosis, and elastic fibers in the STSG group. The cost of the STSG was 3.5 times higher than the ADM group.Conclusions:Acellular dermis grafting for reconstruction of the oral cavity offers several advantages over STSG, including the lack of donor site morbidity, lower cost, a natural appearing mucosal surface, and comparable if not superior functional status. Lower graft survival rates for ADM in the setting of prior radiation and with thicker graft material was encountered. Laryngoscope, 2009
A model for 532‐nanometer pulsed potassium titanyl phosphate (KTP) laser—Induced injury in the rat larynx
Authors: Mallur Pavan S. , Amin Milan R. , Saltman Benjamin E. , Branski Ryan C. 
Published: July 2009

AbstractObjectives/Hypothesis:The potassium titanyl phosphate (KTP) laser is emerging as a potentially effective treatment for various vocal fold pathologies. To date, the precise mechanism(s) of action of this wavelength on the layered microarchitecture of the vocal fold remains unknown. The purpose of this study is to develop an in vivo model for the use of the KTP laser in the rat vocal fold and to characterize the potential of this model for future studies.Study Design:In vivo survival surgery.Methods:A model for videoendoscopic visualization and injury to the rat vocal fold was established using a microlaryngoscope and rigid telescope. Unilateral vocal fold injury was induced with the KTP laser at 10 Watts (W) 20 milliseconds (ms) pulse width. Animals were euthanized at 1 day post‐treatment. Larynges were subjected to gross visual analysis and histological analyses via hematoxylin and eosin and trichrome staining.Results:Consistent endoscopic visualization and injury was obtained without significant operative morbidity or mortality. The KTP laser caused superficial blanching and minor edema in the vocal fold, which resolved grossly by 24 hours postinjury. A modest inflammatory cell infiltrate was observed 1 day following injury. However, no remarkable alterations to the vocal fold microarchitecture were observed in the acute period.Conclusions:We propose that this novel model simulates the clinical scenario of laser use for the vocal folds. Use of this model will allow us to further characterize effects, mechanisms, and therapeutic efficacy of this wavelength. Laryngoscope, 2009
Secondary central compartment surgery for thyroid cancer
Authors: Ondik Michael P. , Dezfoli Seper , Lipinski Lindsay , Ruggiero Francis , Goldenberg David 
Published: July 2009

AbstractObjectives/Hypothesis:To report surgical outcomes in a large series of patients with a history of thyroid cancer who underwent secondary central compartment surgery (SCCS).Study Design:Retrospective chart review.Methods:The records of 44 patients who underwent 47 secondary central compartment surgeries for thyroid cancer were reviewed.Results:Metastatic nodal disease was found in 59.6% (28) central neck compartments. Remnant thyroid tissue was removed from 17 necks. The rate of transient and permanent vocal cord paralysis per SCCS was 2.1% and 6.4%, respectively. Transient and permanent hypoparathyroidism occurred in 11.9% and 9.5% of cases, respectively.Conclusions:SCCS is feasible but does carry some risk. The long‐term implications of early intervention in this setting are still largely unknown and will warrant future research. Laryngoscope, 2009
Effect of vegetation restoration on ant nest‐building activities following mobile dune stabilization in the Horqin Sandy land, Northern China
Authors: Liu R. T. , Zhao H. L. , Zhao X. Y. 
Published: July 2009

AbstractMeasurements of the density and characteristics (size and height) of ant mounds were carried out on mobile, semi‐mobile, semi‐fixed and fixed dunes in the Horqin Sandy Land, Northern China. The relationships between the distribution of ant mounds and the plant community (abundance and cover) were investigated, for areas within and across the dune stages. Changes in spatial pattern of ant mounds were also analysed following mobile dune stabilization. The results showed no ant mounds on mobile dunes; the mound density was significantly higher on fixed dunes than on semi‐fixed or semi‐mobile dunes. The mound density depended on plant density and cover across all dune stages, but not within any dune stage. The mound diameter increased but the mound height decreased from semi‐mobile dunes to fixed dunes. However, the mound diameter and height were not related to plant cover and density within any stabilization stage or across all dune stages. The spatial pattern of ant mounds tended to change from more clumped (semi‐mobile and semi‐fixed dunes) to less clumped and approached a random pattern (fixed dunes) along the dune stabilization gradient, which was related to the changing vegetation pattern during succession. Although the quantification of the number of ant species present was not attempted on each dune, the observed differences in ant colour and size suggest at least eight species were present. Fixed dunes were more attractive for different kinds of ant species, but the mound distribution exhibited a more random pattern with more continuous vegetation. Thus, different environmental conditions, especially in terms of the plant communities present at different dune stages, affected the activities and behaviour of the ants (including the distribution of mounds), but did not affect mound size and height. Copyright © 2009 John Wiley & Sons, Ltd.
Molecular complexes between π‐excedent heterocycles (indoles and carbazole) and π‐deficient polynitrobenzenes
Authors: López Concepción , Claramunt Rosa M. , Pinilla Elena , Torres M. Rosario , Alkorta Ibon , Elguero José 
Published: July 2009

AbstractFive charge‐transfer complexes 1–5 derived from indoles (including a carbazole) and halogenopolynitrobenzenes (ClDNB, FDNB, ClTNB) as well as their individual components have been studied in the solid state by 13C CPMAS NMR. The stacking effects on the 13C chemical shifts have been rationalized by means of M05‐2X functional and GIAO/B3LYP/6‐311 ++G(d,p) calculations. The results, although only semiquantitative, are very promising for studying such structures. Copyright © 2009 John Wiley & Sons, Ltd.
Patient with amyloidoma of the ulnar nerve and salivary glands
Authors: Salameh Johnny , Baran Johanna L. , Tick Chong Peter Siao 
Published: July 2009

AbstractAmyloidomas of the peripheral nervous system have been reported rarely. We describe a patient with a history of localized amyloidosis of the salivary glands who presented a few years later with paresthesias of her left medial arm, forearm, and fifth digit. A mass affecting the left ulnar nerve was confirmed by MRI studies. It was excised and proven on pathological examination to be an amyloidoma. The benign course of this patient's illness is consistent with localized amyloidosis affecting two different organs. Muscle Nerve, 2009
Optimal routing with failure‐independent path protection
Authors: Stidsen Thomas , Petersen Bjørn , Spoorendonk Simon , Zachariasen Martin , Rasmussen Kasper Bonne 
Published: July 2009

AbstractReliable communication has become crucial in today's information society. Modern communication networks are required to deliver reliable communication to their customers. Unfortunately, protection against network failures significantly hampers efficient utilization of network investments, because the associated routing problems become much harder. In this article we present a rigorous mathematical analysis of one of the most promising protection methods: Failure independent path protection. We present an LP model which is solved by column generation. The subproblem is proven to be strongly$ \cal N $P‐hard, but still solvable for medium sized networks through the use of specialized dynamic programming algorithms. This enables us to evaluate the performance of failure independent path protection for eight networks with up to 37 nodes and 57 links. The results indicate that only between 3% and 8% extra network capacity is necessary when compared with the capacity required by complete rerouting (which is the absolute lower bound for single link failure protection). © 2009 Wiley Periodicals, Inc. NETWORKS, 2010
Design of quadrature rules for Müntz and Müntz‐logarithmic polynomials using monomial transformation
Authors: Lombardi Guido 
Published: July 2009

AbstractA method for constructing the exact quadratures for Müntz and Müntz‐logarithmic polynomials is presented. The algorithm does permit to anticipate the precision (machine precision) of the numerical integration of Müntz‐logarithmic polynomials in terms of the number of Gauss–Legendre (GL) quadrature samples and monomial transformation order. To investigate in depth the properties of classical GL quadrature, we present new optimal asymptotic estimates for the remainder. In boundary element integrals this quadrature rule can be applied to evaluate singular functions with end‐point singularity, singular kernel as well as smooth functions. The method is numerically stable, efficient, easy to be implemented. The rule has been fully tested and several numerical examples are included. The proposed quadrature method is more efficient in run‐time evaluation than the existing methods for Müntz polynomials. Copyright © 2009 John Wiley & Sons, Ltd.
Strict and effective bounds in goal‐oriented error estimation applied to fracture mechanics problems solved with XFEM
Authors: Panetier J. , Ladevèze P. , Chamoin L. 
Published: July 2009

AbstractIn this work, we analyze a method that leads to strict and high‐quality local error bounds in the context of fracture mechanics. We investigate in particular the capability of this method to evaluate the discretization error for quantities of interest computed using the extended finite element method (XFEM). The goal‐oriented error estimation method we are focusing on uses the concept of constitutive relation error along with classical extraction techniques. The main innovation in this paper resides in the methodology employed to construct admissible fields in the XFEM framework, which involves enrichments with singular and level set basis functions. We show that this construction can be performed through a generalization of the classical procedure used for the standard finite element method. Thus, the resulting goal‐oriented error estimation method leads to relevant and very accurate information on quantities of interest that are specific to fracture mechanics, such as mixed‐mode stress intensity factors. The technical aspects and the effectiveness of the method are illustrated through two‐dimensional numerical examples. Copyright © 2009 John Wiley & Sons, Ltd.
An essentially non‐oscillatory semi‐Lagrangian method for tidal flow simulations
Authors: El‐Amrani Mofdi , Seaïd Mohammed 
Published: July 2009

AbstractWe develop an essentially non‐oscillatory semi‐Lagrangian method for solving two‐dimensional tidal flows. The governing equations are derived from the incompressible Navier–Stokes equations with assumptions of shallow water flows including bed frictions, eddy viscosity, wind shear stresses and Coriolis forces. The method employs the modified method of characteristics to discretize the convective term in a finite element framework. Limiters are incorporated in the method to reconstruct an essentially non‐oscillatory algorithm at minor additional cost. The central idea consists in combining linear and quadratic interpolation procedures using nodes of the finite element where departure points are localized. The resulting semi‐discretized system is then solved by an explicit Runge–Kutta Chebyshev scheme with extended stages. This scheme adds in a natural way a stabilizing stage to the conventional Runge–Kutta method using the Chebyshev polynomials. The proposed method is verified for the recirculation tidal flow in a channel with forward‐facing step. We also apply the method for simulation of tidal flows in the Strait of Gibraltar. In both test problems, the proposed method demonstrates its ability to handle the interaction between water free‐surface and bed frictions. Copyright © 2009 John Wiley & Sons, Ltd.