bluuebunny/crossref_metadata_2025_split huggingface dataset:
Empirical formulation and parameterization of cation–π interactions for protein modeling
Authors: Du Qi‐Shi , Long Si‐Yu , Meng Jian‐Zong , Huang Ri‐Bo 
Published: October 2011

AbstractCation–π interaction is comparable and as important as other main molecular interaction types, such as hydrogen bond, electrostatic interaction, van der Waals interaction, and hydrophobic interaction. Cation–π interactions frequently occur in protein structures, because six (Phe, Tyr, Trp, Arg, Lys, and His) of 20 natural amino acids and all metallic cations could be involved in cation–π interaction. Cation–π interactions arise from complex physicochemical nature and possess unique interaction behaviors, which cannot be modeled and evaluated by existing empirical equations and force field parameters that are widely used in the molecular dynamics. In this study, the authors present an empirical approach for cation–π interaction energy calculations in protein interactions. The accurate cation–π interaction energies of aromatic amino acids (Phe, Tyr, and Try) with protonated amino acids (Arg and Lys) and metallic cations (Li+, Na+, K+, and Ca2+) are calculated using B3LYP/6‐311+G(d,p) method as the benchmark for the empirical formulization and parameterization. Then, the empirical equations are built and the parameters are optimized based on the benchmark calculations. The cation–π interactions are distance and orientation dependent. Correspondingly, the empirical equations of cation–π interactions are functions of two variables, the distance r and the orientation angle θ. Two types of empirical equations of cation–π interactions are proposed. One is a modified distance and orientation dependent Lennard–Jones equation. The second is a polynomial function of two variables r and θ. The amino acid‐based empirical equations and parameters provide simple and useful tools for evaluations of cation–π interaction energies in protein interactions. © 2011 Wiley Periodicals, Inc. J Comput Chem , 2011
Micro‐structural tissue analysis for automatic histopathological image annotation
Authors: Díaz Gloria , Romero Eduardo 
Published: October 2011

AbstractThis article presents a new approach for extracting high level semantic concepts from digital histopathological images. This strategy provides not only annotation of several biological concepts, but also a coarse location of these concepts. The proposed approach is composed of five main steps: (1) a stain decomposition stage, which separates the contribution of hematoxylin and eosin dyes, (2) a color standardization that corrects color image differences, (3) a part‐based representation, which describes the image in terms of the conditional probability of relevant local patches, selected by their stain contributions, (4) a discriminative classification model, which bridges out the found patterns and the biological concepts, (5) a block‐based annotation strategy that identifies the multiple biological concepts within an image. A set of 655 skin images, containing 10 biological concepts of skin tissues were used for assessing the proposed approach, obtaining a sensitivity of 84% and a specificity of 67% when annotating images with multiple concepts. Microsc. Res. Tech., 2011. © 2011 Wiley Periodicals, Inc.
Automatic segmentation on multiple starch granules from microscopic images
Authors: Guo Shengwen 
Published: October 2011

AbstractStarch is the most important carbohydrate in the human diet and contained in many staple foods such as rice, wheat, corn, potatoes and cassava, etc. Currently, microscopic imaging technology is one of the most effective ways to investigate and analyze the structure of starches. Segmentation of starch granules is a necessary step for starch granule structure analysis such as starch granules detection, shape recognition, and size computation. This article investigates a new method based on GVF (gradient vector flow) snake deformable model for starch granules segmentation. The proposed method focuses on full automatic segmentation on granules, especially on separation of adjacent and contacted starch granules, which occur widely in microscopic images. A novel energy function based on position and intensity is introduced into the directional gradient computation, thus the directional gradient is used to obtain the directional GVF snake, which drives the deforming contours to the real contours of multiple granules. To demonstrate the good ability of the proposed method, we segment 30 starch granule images and compare it with the level set method, experimental results show that the new method can separate multiple starch granules successfully; especially it works much better on overlapping objects segmentation than the level set method. Microsc. Res. Tech. 2011. © 2011 Wiley‐Liss, Inc.
Contribution of body mass index to postoperative outcome in minority patients
Authors: Nafiu Olubukola O. , Ramachandran Satya Krishna , Wagner Deborah S. , Campbell Darrell A. , Stanley James C. 
Published: October 2011

AbstractOBJECTIVE:The purpose of this investigation was to examine the association of body mass index (BMI) category with short‐term outcomes in minority surgical patients—a relationship that previously has not been well characterized.METHODS:Data from the National Surgical Quality Improvement Program were used to calculate the BMI of minority patients undergoing surgery from 2005 to 2008. Patients were stratified into 5 BMI classes. Stepwise logistic regression was used to calculate odds ratios for mortality after controlling for known clinically relevant covariates.MAIN OUTCOME MEASURES:Morbidity and mortality at 30 days, across all 5 BMI classes.RESULTS:Among 119,619 minority patients studied, 50% were African American, 36% Hispanic, 10% Asian and Pacific Islanders, and 4% American Indian and Alaskan natives. Seventy percent were overweight or obese. Women were more likely to be obese or severely obese. The overall mortality rate was 1.5%, and this varied significantly by BMI class. Distribution of 30‐day mortality demonstrated a progressive decrease, with the highest risk of death in the underweight class, and the lowest risk of death in the severely obese class. This relationship was maintained, even in patients with at least 1 major postoperative complication.CONCLUSION:The prevalence of being overweight or obese was high in this nationally representative cohort of minority surgical patients. Although BMI class is a significant predictor of 30‐day mortality, the effect appeared paradoxical. The poorest outcomes were in the underweight and normal BMI patients. Severely obese patients had the lowest risk of mortality, even after experiencing a major postoperative complication. Journal of Hospital Medicine 2012; © 2011 Society of Hospital Medicine.
High‐resolution ultrashort echo time (UTE) imaging on human knee with AWSOS sequence at 3.0 T
Authors: Qian Yongxian , Williams Ashley A. , Chu Constance R. , Boada Fernando E. 
Published: October 2011

AbstractPurpose:To demonstrate the technical feasibility of high‐resolution (0.28–0.14 mm) ultrashort echo time (UTE) imaging on human knee at 3T with the acquisition‐weighted stack of spirals (AWSOS) sequence.Materials and Methods:Nine human subjects were scanned on a 3T MRI scanner with an 8‐channel knee coil using the AWSOS sequence and isocenter positioning plus manual shimming.Results:High‐resolution UTE images were obtained on the subject knees at TE = 0.6 msec with total acquisition time of 5.12 minutes for 60 slices at an in‐plane resolution of 0.28 mm and 10.24 minutes for 40 slices at an in‐plane resolution of 0.14 mm. Isocenter positioning, manual shimming, and the 8‐channel array coil helped minimize image distortion and achieve high signal‐to‐noise ratio (SNR).Conclusion:It is technically feasible on a clinical 3T MRI scanner to perform UTE imaging on human knee at very high spatial resolutions (0.28–0.14 mm) within reasonable scan time (5–10 min) using the AWSOS sequence. J. Magn. Reson. Imaging 2012;35:204‐210. © 2011 Wiley Periodicals, Inc.
Anterior cervical interbody constructs: effect of a repetitive compressive force on the endplate
Authors: Ordway Nathaniel R. , Rim Byeong Cheol , Tan Rong , Hickman Rebecca , Fayyazi Amir H. 
Published: October 2011

AbstractGraft subsidence following anterior cervical reconstruction can result in the loss of sagittal balance and recurring foraminal stenosis. This study examined the implant–endplate interface using a cyclic fatigue loading protocol in an attempt to model the subsidence seen in vivo. The superior endplate from 30 cervical vertebrae (C3 to T1) were harvested and biomechanically tested in axial compression with one of three implants: Fibular allograft; titanium mesh cage packed with cancellous chips; and trabecular metal. Each construct was cyclically loaded from 50 to 250 N for 10,000 cycles. Nondestructive cyclic loading of the cervical endplate–implant construct resulted in a stiffer construct independent of the type of the interbody implant tested. The trabecular metal construct demonstrated significantly more axial stability and significantly less subsidence in comparison to the titanium mesh construct. Although the allograft construct resulted in more subsidence than the trabecular metal construct, the difference was not significant and no difference was found when comparing axial stability. For all constructs, the majority of the subsidence during the cyclic testing occurred during the first 500 cycles and was followed by a more gradual settling in the remaining 9,500 cycles. © 2011 Orthopaedic Research Society. © 2011 Orthopaedic Research Society Published by Wiley Periodicals, Inc. J Orthop Res 30:587–592, 2012
Possibilities of enhancing the colour of egg yolk
Authors: Dvořák Petr , Suchý Pavel , Straková Eva , Kopřiva Vladimír 
Published: October 2011

AbstractBACKGROUND: This study attempts to compare two possibilities of enhancing the colour of egg yolk. One of them is based on the ecological rearing of laying hens on natural green grass whereas the other uses a feeding dose supplemented with natural pigments in laying hens reared in individual cages. Is it possible to distinguish these two technologies using yolk colour determination in the CIELAB system?RESULTS: Yolk colour parameters such as L*, a*, and b* in the group of grazed hens are significantly different (α = 0.001) from those observed in hens reared in cages. The yolk colour shows a darker, redder and more yellow colour. The greatest difference was seen in the red colour parameter, a*, that increased more than twice. Visually, this means a shift towards a more orange colour. Compared to grazing in the meadow (ΔE* = 13.257), the addition of artificial pigments in the feed resulted in a more significant increase in the parameter ΔE* (CIE total colour difference), with the greatest value of ΔE* being observed with the use of both pigments (ΔE* = 24.265).CONCLUSION: Grazing increases the parameter a* whereas the values of the parameter C*ab remain relatively low. The parameter ΔE* is significantly lower in the case of grazing as compared to the supplementation of the feed with pigments. However, colourity parameters cannot be used as a specific standard to identify a particular grazing technology as their values vary during the laying period. Copyright © 2011 Society of Chemical Industry
Identification and proteomic analysis of a novel gossypol‐degrading fungal strain
Authors: Yang Xia , Sun Jian‐Yi , Guo Jian‐Lin , Weng Xiao‐Yan 
Published: October 2011

AbstractBACKGROUND: Cottonseed meal, an important source of feed raw materials, has limited use in the feed industry because of the presence of the highly toxic gossypol. The aim of the current work was to isolate the gossypol‐degrading fungus from a soil microcosm and investigate the proteins involved in gossypol degradation.RESULTS: A fungal strain, AN‐1, that uses gossypol as its sole carbon source was isolated and identified as Aspergillus niger. A large number of intracellular proteins were detected using sodium dodecyl sulfate–polyacrylamide gel electrophoresis, but no significant difference was observed between the glucose‐containing and gossypol‐containing mycelium extracts. Two‐dimensional gel electrophoresis results showed that the protein spots were concentrated in the 25.0–66.2 kDa range and distributed in different pI gradients. PDQuest software showed that 51 protein spots in the gels were differentially expressed. Of these, 20 differential protein spots, including six special spots expressed in gossypol, were analyzed using matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry.CONCLUSION: The fungus AN‐1 biodegraded gossypol and the proteomic analysis results indicate that some proteins were involved in the gossypol biodegradation during fungus survival, using gossypol as its sole carbon source. Copyright © 2011 Society of Chemical Industry
Composition of meat and offal from weaned and fattened rabbits and results of stereospecific analysis of triacylglycerols and phosphatidylcholines
Authors: D'Arco Gilda , Blasi Francesca , Cossignani Lina , Di Giacomo Franco , Ciavardelli Domenico , Ventura Francesca , Scipioni Silvia , Simonetti Maria Stella , Damiani Pietro 
Published: October 2011

AbstractBACKGROUND: Rabbit meat has excellent nutritive properties. The purpose of this study was to characterize rabbit meat and offal; in particular, the lipid fraction was studied in order to evaluate total and positional fatty acid (FA) compositions of triacylglycerol (TAG) and phosphatidylcholine (PC) fractions. Eight samples of weaned and eight of fattened rabbits were considered.RESULTS: Fattened rabbit meat contained slightly higher protein percentage content (P < 0.05) in comparison to weaned (20.1% versus 18.0%). Calcium content was higher in meat than in offal, unlike sodium, iron, zinc, manganese and copper. The cholesterol content in offal was much higher than in meat. FA profiles of total lipid showed a high percentage of unsaturated fatty acids and an n‐6/n‐3 ratio of 10.3 for fattened rabbit meat. Stereospecific analysis of TAG and PC was carried out on an eight‐sample pool of each meat and offal from weaned and fattened rabbits. In all samples the sn‐2‐position was prevalently esterified with oleic and linoleic acids in TAG, with polyunsaturated fatty acids in PC.CONCLUSION: Lipids from rabbit meat presented higher content of monounsaturated FA and lower n‐6/n‐3 ratio in comparison to offal, which was characterized by higher cholesterol and mineral levels. Copyright © 2011 Society of Chemical Industry
Supercritical extraction of phloroglucinol and benzophenone derivatives from Hypericum carinatum: Quantification and mathematical modeling
Authors: Barros Francisco M. C. , Silva Flávia C. , Nunes Jéssica M. , Vargas Rubem M. F. , Cassel Eduardo , von Poser Gilsane L. 
Published: October 2011

AbstractThe aerial parts of Hypericum carinatum (Guttiferae) were extracted with supercritical carbon dioxide under constant temperature (40, 50 or 60°C) and gradual pressure increase (90, 120, 150 and 200 bar) aiming at the recovery of enriched fractions containing uliginosin B, cariphenone A and cariphenone B, compounds of pharmaceutical interest. The yields of these substances were determined by high‐performance liquid chromatography and compared with those obtained with n‐hexane maceration. The supercritical‐fluid extraction showed higher selectivity than the conventional solvent extraction method. After defining 40°C and 90 bar as the best conditions to obtain the target compounds, a mathematical model was used for the extraction process and a good correlation was achieved with the experimental data.
Simply and effectively preparing high‐purity phosvitin using polyethylene glycol and anion‐exchange chromatography
Authors: Zhang Xiaowei , Qiu Ning , Geng Fang , Ma Meihu 
Published: October 2011

AbstractAn attempt was made to develop a new protocol for preparing phosvitin that could be easy scaled up using polyethylene glycol (PEG6000). Influence of PEG6000 concentration and pH of sample solution on phosvitin isolation was investigated. Phosvitin of high purity (99%) was obtained in good yield (47%) with the optimal condition of pH 4.0 and 3% PEG6000 precipitation. In addition, through evaluating different anion‐exchange chromatography methods, the DEAE procedure at pH 7.5 was finally selected as the best procedure to obtain metal‐free phosvitin that lost the least protein. Furthermore, it is observed that the purity and characterizations of prepared phosvitin were similar to those of the standard phosvitin from Sigma, and the random coil of phosvitin converted into more compact structure after removing metal ion. In conclusion, the developed method was simple and suitable for scaled up preparation of phosvitin.
Oxygen vacancy related relaxation and conduction behavior in (1 − x) NBT‐xBiCrO3 solid solution
Authors: Selvamani R. , Singh G. , Tiwari V. S. , Gupta P. K. 
Published: October 2011

AbstractThe ac‐conductivity measurements carried out on (1 − x)NBT‐xBiCrO3 solid solution in the radio frequency range. The conductivity measurements suggest that with increase in BiCrO3 content the electrical conductivity of sodium bismuth titanate (Na0.5Bi0.5TiO3) (NBT) increases. For x = 0.10 and 0.15 two relaxation behaviors are observed, related to long range conduction and short range hopping of defects. Activation energy calculated from dielectric relaxation as well as conductivity data reveals that both the processes are due to oxygen defects formed by substitution of chromium at titanium site. A reasonable decrease in the conductivity and dielectric loss were observed after oxygen annealing of the samples. Presence of relaxation peaks even after oxygen annealing suggests that relaxation is mainly by extrinsic oxygen defects produced due to substitution of chromium.
Application of statistical dynamical diffraction theory to highly defective ion implanted SiGe heterostructures
Authors: Shreeman P. K. , Matyi R. J. 
Published: October 2011

AbstractThe statistical dynamical diffraction theory (SDDT) provides a method for performing high resolution X‐ray diffraction (HRXRD) analyses from materials that contain high levels of structural imperfection. SDDT is implemented by combining kinematical and dynamical diffraction formalisms into a single framework through the inclusion of two parameters (a static Debye–Waller factor and a correlation length) that can provide an adjustable coupling between the kinematic and dynamic extremes. Typically one of the prominent difficulties in implementing SDDT is the mathematical complexities that are characteristic of this theory. Recently we have demonstrated a simplified realization of SDDT [Shreeman and Matyi, J. Appl. Crystallogr. 43, 550 (2010)] that preserves the essential features of the theory while allowing it to be applied to a variety of structures. Here we show the viability of this approach by fitting various experimental HRXRD data from highly defective and partially relaxed Si0.70Ge0.30 ion implanted heterostructures. This study demonstrates the capabilities the SDDT theory provides for HRXRD analyses of highly defective semiconductor materials.
Recent developments of anomalous X‐ray scattering for non‐crystalline materials with help of reverse Monte Carlo modeling: The example of GeSe2 glass
Authors: Hosokawa Shinya , Pilgrim Wolf‐Christian , Bérar Jean‐François , Kohara Shinji 
Published: October 2011

AbstractAnomalous X‐ray scattering (AXS) experiments on glassy GeSe2 were carried out at energies close to the Ge and Se K absorption edges in order to explore the atomic structure in the short‐ and intermediate‐ranges. The partial structure factors, Sij(Q), and the corresponding partial pair‐distribution functions, gij(r), obtained with help of reverse Monte Carlo (RMC) modeling, are in good agreement with the experimental results from neutron diffraction employing isotopic substitution (NDIS), and with the theoretical data from ab initio molecular dynamics simulation. The prepeak in the total structure factor, S(Q), indicating the existence of intermediate‐range order (IRO), does not only result from Ge–Ge atomic correlations, but also contains Ge–Se correlations. From the atomic configuration obtained from RMC modeling, several structural parameters are discussed, such as partial coordination numbers, connections of the Ge(Se1/2)4 tetrahedra, and bond angle distributions.
Rheology of a suspension of elastic particles in a viscous shear flow
Authors: Gao Tong , Hu Howard H. , Castañeda Pedro Ponte 
Published: October 2011

AbstractIn this paper we consider a suspension of elastic solid particles in a viscous liquid. The particles are assumed to be neo-Hookean and can undergo finite elastic deformations. A polarization technique, originally developed for analogous problems in linear elasticity, is used to establish a theory for describing the finite-strain, time-dependent response of an ellipsoidal elastic particle in a viscous fluid flow under Stokes flow conditions. A set of coupled, nonlinear, first-order ODEs is obtained for the evolution of the uniform stress fields in the particle, as well as for the shape and orientation of the particle, which can in turn be used to characterize the rheology of a dilute suspension of elastic particles in a shear flow. When applied to a suspension of cylindrical particles with initially circular cross-section, the theory confirms the existence of steady-state solutions, which can be given simple analytical expressions. The two-dimensional, steady-state solutions for the particle shape and orientation, as well as for the effective viscosity and normal stress differences in the suspension, are in excellent agreement with direct numerical simulations of multiple-particle dispersions in a shear flow obtained by using an arbitrary Lagrangian–Eulerian (ALE) finite element method (FEM) solver. The corresponding solutions for the evolution of the microstructure and the rheological properties of suspensions of initially spherical (three-dimensional) particles in a simple shear flow are also obtained, and compared with the results of Roscoe (J. Fluid Mech., vol. 28, 1967, pp. 273–293) in the steady-state regime. Interestingly, the results show that sufficiently soft elastic particles can be used to reduce the effective viscosity of the suspension (relative to that of the pure fluid).