bluuebunny/crossref_metadata_2025_split huggingface dataset:
MATCH: An atom‐typing toolset for molecular mechanics force fields
Authors: Yesselman Joseph D. , Price Daniel J. , Knight Jennifer L. , Brooks Charles L. 
Published: November 2011

AbstractWe introduce a toolset of program libraries collectively titled multipurpose atom‐typer for CHARMM (MATCH) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion of multiple chemical structure file formats into a molecular graph. A general chemical pattern‐matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges, and force field parameters are achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom‐type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment‐based property prediction. In this work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond charge increment rules derived from one force field can be transferred to another. In addition, using leave‐one‐out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM general force field (Vanommeslaeghe, et al., J Comput Chem 2010, 31, 671), one million molecules from the PubChem database of small molecules are typed, parameterized, and minimized. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Theoretical investigation on redox‐switchable second‐order nonlinear optical responses of push–pull Cp*CoEt2C2B4H3‐expanded (metallo)porphyrins
Authors: Ma Nana , Liu Chunguang , Qiu Yongqing , Sun Shiling , Su Zhongmin 
Published: November 2011

AbstractThe second‐order nonlinear optical (NLO) properties of the Cp*Co(C2H5)2C2B4H3‐expanded (metallo)porphyrins (Cp* = C5Me5) have been investigated by using ab inito RHF and density functional theory (DFT) methods. The investigation shows that the compound with expand porphyrin possesses remarkable large molecular hyperpolarizability βtot value, ∼414.1 × 10−30 esu (at LC‐ωPBE level), and might be an excellent second‐order NLO material. From the character of charge transfer (CT) transition, it indicates that the −Cp*Co(C2H5)2C2B4H3 acts as an electron donor in this kind of systems. As a result of the redox behavior on expanded (metallo)porphyrin, the redox switching character of the NLO responses for the systems 2a–4a has also been studied. The results show that the βtot values of reduced forms are larger than that of neutral ones. Furthermore, the time‐dependent DFT calculation illustrates that reduced forms have a significant difference on the CT patterns versus neutral ones. The present investigation provides insight into the comparison with DFT results on estimating first hyperpolarizability and the NLO properties of the series of push–pull compounds. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Mechanism for the reaction of 2‐naphthol with N‐methyl‐N‐phenyl‐hydrazine suggested by the density functional theory investigations
Authors: Gao Jie Ying , Zhang Cheng Hua , Luo Mei Ming , Kim Chan Kyung , Chu Wei , Xue Ying 
Published: November 2011

AbstractFor the first time the computed mechanisms for the novel reaction of 2‐naphthol with N‐methyl‐N‐phenylhydrazine, leading to 1‐amino‐2‐naphthol (Tang et al., J Am Chem Soc 2008, 130, 5840), have been investigated using the density functional theory. Four distinct possible pathways were evaluated: two amination mechanisms with the attack of NH2 group respectively at the α‐position C1 and β‐position C3 atoms of 2‐naphthol (pathways 1 and 2) as well as two rearrangement processes with displacement of the phenolic hydroxyl group followed by the benzidine‐like rearrangement at the α‐position C1 and β‐position C3 atoms of 2‐naphthol, respectively (pathways 3 and 4). Solvent effect has been tested based on the optimized geometries of the stationary points in solution at the B3LYP/PCM/6‐31+G(d,p) level of theory with an averaged dielectric constant of binary solvent. Single‐point energies of the optimized structures have been calculated using three hybrid density functionals, B3LYP, MPW3LYP, and B3PW91 with the 6‐311++G(3df,2p) basis set. Our computed results clearly manifest that pathway 1 (α‐amination) has the highest possibility to occur, with the Gibbs free energies being lower by 6 to 20 kcal/mol compared with the other three pathways, which leads to 1‐amino‐2‐naphthol and N‐methylaniline as products. It is in excellent agreement with the experimental observation. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Proton MR spectroscopy in predicting the increase of perfusion MR imaging for WHO grade II gliomas
Authors: Guillevin Remy , Menuel Carole , Abud Lucas , Costalat Robert , Capelle Laurent , Hoang‐Xuan Khê , Habas Christophe , Chiras Jacques , Vallée Jean‐Noel 
Published: November 2011

AbstractPurpose:To investigate the correlation between the metabolite ratios obtained from proton magnetic resonance (MR) spectroscopy and those obtained from MR perfusion parameters (relative cerebral blood volume [rCBV]) in a cohort of low‐grade glioma (LGG).Materials and Methods:Patients underwent prospectively conventional MR, proton magnetic resonance spectroscopy (1HMRS), and perfusion‐weighted images (PWI). Statistical analyses were performed to determine the correlative and independent predictive factors of rCBVmax and the metabolite ratio thresholds with optimum sensitivity and specificity.Results:Thirty‐one patients were included in this study. Linear correlations were observed between the metabolic ratios (lactate [Lac]/creatine [Cr], choline [Cho]/N‐acetyl‐aspartate [NAA], free‐lipids/Cr) and rCBVmax (P < 0.05). These metabolic ratios were determined to be independent predictive factors of rCBVmax (P = 0.027, 0.011 and 0.032, respectively). According to the receiver operating characteristic curves, the cutoff values of the metabolic ratios to discriminate between the two populations of rCBVmax (<1.7 versus = 1.7) were 1.72, 1.54, and 1.40, respectively, with a sensitivity = 75% and a specificity >95% for Lac/Cr.Conclusion:This study demonstrated consistent correlations between the data from 1HMRS and PWI. The Lac/Cr ratio predicts regional hemodynamic changes, which are themselves a useful biomarker of clinical prognosis in patients with LGG. As such, this ratio may provide a new parameter for making improved clinical decisions. J. Magn. Reson. Imaging 2012;35:543‐550. © 2011 Wiley Periodicals, Inc.
Measuring T2 in vivo with J‐difference editing: Application to GABA at 3 tesla
Authors: Edden Richard A.E. , Intrapiromkul Jarunee , Zhu He , Cheng Ying , Barker Peter B. 
Published: November 2011

AbstractPurpose:To develop an experimental approach for determining in vivo transverse relaxation rates (T2) of metabolites that are detected by spectral editing without using simulations, and to demonstrate this approach to measure the T2 of γ‐aminobutyric acid (GABA).Materials and Methods:The proposed method first determines the TE‐dependence of the edited signals using measurements in a pure phantom solution (10 mM γ‐aminobutyric acid; GABA); the phantom T2 is also determined. Once the editing echo time (TE) ‐modulation pattern is known, it can then be used to determine T2 in vivo. The method was applied to measure GABA T2 in the occipital lobe of five healthy adult subjects at 3T, using a J‐difference editing method. Unwanted macromolecular contributions to the GABA signal were also measured.Results:The in vivo T2 of edited GABA signal was 88 ± 12 ms; this preliminary result is somewhat shorter than other metabolite T2 values in the literature at this field strength.Conclusion:Spectral editing methods are now widely used to detect low concentration metabolites, such as GABA, but to date no edited acquisition methods have been proposed for the measurement of transverse relaxation times (T2). The method described has been successfully applied to measuring the T2 of GABA. J. Magn. Reson. Imaging 2012;35:229‐234. © 2011 Wiley Periodicals, Inc.
Quantifying hemodynamic refractory bold effects in normal subjects at the single‐subject level using an inverse logit fitting procedure
Authors: Descamps Benedicte , Vandemaele Pieter , Reyngoudt Harmen , Deblaere Karel , Leybaert Luc , Paemeleire Koen , Achten Eric 
Published: November 2011

AbstractPurpose:To evaluate whether hemodynamic refractory effects provoked by repeated visual stimulation can be detected and quantified at the single‐subject level using a recently described hemodynamic response function (HRF) fitting algorithm.Materials and Methods:Hemodynamic refractory effects were induced with an easily applicable functional MRI (fMRI) paradigm. A fitting method with inverse logit (IL) functions was applied to quantify net HRFs at the single‐subject level with three interstimulus intervals (ISI; 1, 2, and 6 s). The model yielded amplitude, latencies, and width for each HRF.Results:HRF fitting was possible in 44 of 51 healthy volunteers, with excellent goodness‐of‐fit (R2 = 0.9745 ± 0.0241). Refractory effects were most pronounced for the 1‐s ISI (P < 0.001) and had nearly disappeared for the 6‐s ISI.Conclusion:Quantifying refractory effects in individuals was possible in 86.3% of normal subjects using the IL fitting algorithm. This setup may be suitable to explore such effects in individual patients. J. Magn. Reson. Imaging 2012;35:723‐730. © 2011 Wiley Periodicals, Inc.
Gadofluorine M enhanced MRI in experimental glioma: Superior and persistent intracellular tumor enhancement compared with conventional MRI
Authors: Jestaedt Leonie , Lemke Dieter , Weiler Markus , Pfenning Philipp‐Niclas , Heiland Sabine , Wick Wolfgang , Bendszus Martin 
Published: November 2011

AbstractPurpose:To compare conventional magnetic resonance imaging (MRI) techniques (T2‐w and Gadolinium‐DTPA‐enhanced T1‐w images) and Gadofluorine‐M (GfM), a novel contrast agent in MRI, in murine gliomas.Materials and Methods:Growth monitoring of murine gliomas (induced in mice) was performed on a 2.3 Tesla Bruker Biospec MRI unit. First all animals were investigated with conventional MRI techniques. In group I GfM was applied at an early stage of disease, in group II at a later stage. After injection of GfM follow‐up MRI was performed without further injection of contrast agent. On MR images tumor size and signal intensities were assessed. Animals were killed for histological evaluation.Results:In both groups GfM delineated tumor extents larger and more precisely than conventional MRI techniques. The difference between GfM and conventional MRI techniques reached level of significance at both tumor stages. Follow‐up MRI after singular injection of GfM showed persistence of GfM in tumor tissue. On tissue sections GfM‐enhancing areas corresponded closely to vital tumor tissue. GfM showed a mainly intracellular accumulation.Conclusion:Application of GfM resulted in superior delineation of experimental glioma compared with conventional MRI techniques. Thus, GfM bears a high potential in clinical application. J. Magn. Reson. Imaging 2012;35:551‐560. © 2011 Wiley Periodicals, Inc.
The moisture and temperature effect on mechanical performance of flax/starch composites in quasi‐static tension
Authors: Spārniņš E. , Pupurs A. , Varna J. , Joffe R. , Nättinen K. , Lampinen J. 
Published: November 2011

AbstractThe effect of temperature and moisture on mechanical behavior of flax fiber/starch based composites was investigated experimentally. Elastic modulus, the nonlinear tensile loading curves, and failure strain were analyzed. Neat matrix and composites with 20 and 40% weight content of fibers were tested. It was found, performing tests with different amplitudes, that microdamage development with stress is rather limited and the related elastic modulus reduction in this type of composites is not significant. It was shown that the composite elastic modulus and failure stress are linearly related to the maximum tensile stress in resin. The sensitivity of the maximum stress of the resin with respect to temperature and moisture is the source of composites sensitivity to these parameters. Constant interface stress shear lag model for stress transfer assuming matrix yielding at the fiber/matrix interface has been successfully used to explain the tensile test data. It indicates that the sensitivity of the used composite with respect to the matrix properties change could be significantly reduced by increasing the average fiber length from 0.9 mm to 1.5 mm. POLYM. COMPOS., 2011. © 2011 Society of Plastics Engineers
Nanocomposites based on vermiculite clay and ternary blend of poly(L‐lactic acid), poly(methyl methacrylate), and poly(ethylene oxide)
Authors: Auliawan Andi , Woo Eamor M. 
Published: November 2011

AbstractVermiculite (VMT) as clay was introduced into a ternary polymer blend composed of poly(L‐lactic acid) (PLLA), poly(methyl methacrylate) (PMMA), and poly(ethylene oxide) (PEO), whose ternary miscibility was proven within low certain contents of PMMA and PEO in PLLA. VMT was incorporated to the ternary polymer blend as matrix after proper organic modification on the clay. The organically modified vermiculite (OVMT) shows good interaction and acceptable dispersion in the ternary polymer matrix without altering the crystal structures of PLLA/PEO constituents. The effect of OVMT addition was then analyzed in isothermal crystallization by using the Avrami kinetic analysis, and the addition of OVMT is evident in altering nucleation process of the polymer blend as well as the crystal perfection. The activation energy is much lowered by the addition of OVMT, as evident from the analysis; the overall crystallization kinetic rates are increased with the incorporation of OVMT. POLYM. COMPOS., 2011. © 2011 Society of Plastics Engineers
Preparation and flame retardancy of a novel flame‐retardant poly(ethylene‐co‐vinyl acetate)/aluminum hydroxide composites containing phosphorus
Authors: Zhang Jian‐Yao 
Published: November 2011

AbstractA novel flame‐retardant (SPDH) containing phosphorus was synthesized through the reaction of 10‐(2,5‐dihydroxyphenyl)‐9,10‐dihydro‐9‐oxa‐10‐phosphaphenanthrene‐10‐oxide and synthesized intermediate product 3,9‐dichloro‐2,4,8,10‐tetraoxa‐3,9‐diphosphaspiro[5.5] undecane‐3,9‐dioxide, which was used for optimizing the flame retardancy of ethylene‐vinyl acetate copolymer (EVM) rubber/aluminum hydroxide (ATH) composites. The microstructure of SPDH was characterized and determined by Fourier transform infrared and nuclear magnetic resonance spectroscopy. Thermogravimetric analysis (TGA) showed that SPDH had good charring effect at high temperature (600°C). The flame retardancy of the optimized EVM/ATH composites by SPDH was investigated by limiting oxygen index (LOI), cone calorimeter, and UL‐94 vertical burning tests. A higher LOI value (29.8%) and better UL‐94 rating (V‐0) can be achieved for the optimized EVM/ATH composite (EVM‐7) than EVM/ATH composite without SPDH (EVM‐3) with the total loading of additives. The heat release rate decreased and residual mass increased gradually as the loading of SPDH increased for the optimized EVM/ATH composites. There existed distinct synergistic flame‐retardant effect between SPDH and ATH in EVM matrix. POLYM. COMPOS., 2011. © 2011 Society of Plastics Engineers
Optical and electrical properties of polyaniline‐cadmium sulfide nanocomposite
Authors: Ghoswami M. , Ghosh R. , Chakraborty G. , Gupta K. , Meikap A.K. 
Published: November 2011

AbstractPolyaniline‐cadmium sulfide nanocomposite has been synthesized by the chemical oxidative polymerization of aniline with ammonium peroxodisulfate as an initiator in presence of cadmium sulfide nanoparticles. TEM, XRD, FTIR, TGA, UV–vis spectroscopy, and photoluminescence studies were done for the structural, thermal and optical characterization of the samples. The particle size of nanocomposites lies in between 7 and 10 nm. XRD spectrum shows that polyaniline is amorphous, but peaks present in the spectrum of polymer nanocomposites are for cadmium sulfide nanoparticles. TGA result shows that nanocomposite is more thermally stable. The band gap of nanocomposite decreases with increasing content of cadmium sulfide nanoparticles. An enhancement in photoluminescence has been observed in the nanocomposite than that in pure polyaniline. The dc and ac electronic transport property of polyaniline cadmium sulfide composites has been investigated within a temperature range 77 ≤ T ≤ 300 K and in the frequency range 20 Hz–1 MHz. The dc conductivity follows variable range hopping (VRH) model. The ac conductivity follows a power law whereas the temperature dependence of frequency exponent s can be explained by correlated barrier hopping (CBH) model. The dielectric behavior of the samples has been explained in terms of the grain and grain boundary resistance and capacitance. POLYM. COMPOS., 2011. © 2011 Society of Plastics Engineers
The Role of Human Leukocyte Antigen Matching in the Development of Multiethnic “Haplobank” of Induced Pluripotent Stem Cell Lines
Authors: Gourraud Pierre-Antoine , Gilson Leena , Girard Mathilde , Peschanski Marc 
Published: November 2011

Abstract
Among the tools of regenerative medicine, induced pluripotent stem cells (iPSCs) are interesting because the donor genotype can be selected. The construction of banks of iPSC cell lines selected from human leukocyte antigen (HLA) homozygous donors has been proposed to be an effective way to match a maximal number of patients receiving cell therapy from iPSC lines. However, what effort would be required to constitute such a bank for a worldwide application has remained unexplored. We developed a probabilistic model to compute the number of donors to screen for constituting banks of best-chosen iPSC lines with homozygous HLA haplotypes (haplobanks) in four ancestry backgrounds. We estimated what percentage of the patients would be provided with single HLA haplotype matched cell lines. Genetic diversity leads to different outcomes for the four sets in all terms. A bank comprising iPSC lines representing the 20 most frequent haplotypes in each population would request quite different number of donors to screen, between 26,000 for European Americans and 110,000 for African Americans. It would also match different fractions of the recipient population, namely, more than 50% of the European Americans and 22% of African Americans. Conversely, a bank comprising the 100 iPSC lines with the most frequent HLA in each population would leave out only 22% of the European Americans, but 37% of the Asians, 48% of the Hispanics, and 55% of the African Americans. The constitution of a haplobank of iPSC lines is achievable through a large-scale concerted worldwide collaboration.
Disclosure of potential conflicts of interest is found at the end of this article.
Agreement and reliability of pelvic floor measurements during contraction using three‐dimensional pelvic floor ultrasound and virtual reality
Authors: Speksnijder L. , Rousian M. , Steegers E. A. P. , Van Der Spek P. J. , Koning A. H. J. , Steensma A. B. 
Published: November 2011

AbstractObjectivesVirtual reality is a novel method of visualizing ultrasound data with the perception of depth and offers possibilities for measuring non‐planar structures. The levator ani hiatus has both convex and concave aspects. The aim of this study was to compare levator ani hiatus volume measurements obtained with conventional three‐dimensional (3D) ultrasound and with a virtual reality measurement technique and to establish their reliability and agreement.Methods100 symptomatic patients visiting a tertiary pelvic floor clinic with a normal intact levator ani muscle diagnosed on translabial ultrasound were selected. Datasets were analyzed using a rendered volume with a slice thickness of 1.5 cm at the level of minimal hiatal dimensions during contraction. The levator area (in cm2) was measured and multiplied by 1.5 to get the levator ani hiatus volume in conventional 3D ultrasound (in cm3). Levator ani hiatus volume measurements were then measured semi‐automatically in virtual reality (cm3) using a segmentation algorithm. An intra‐ and interobserver analysis of reliability and agreement was performed in 20 randomly chosen patients.ResultsThe mean difference between levator ani hiatus volume measurements performed using conventional 3D ultrasound and virtual reality was 0.10 (95% CI, − 0.15 to 0.35) cm3. The intraclass correlation coefficient (ICC) comparing conventional 3D ultrasound with virtual reality measurements was > 0.96. Intra‐ and interobserver ICCs for conventional 3D ultrasound measurements were > 0.94 and for virtual reality measurements were > 0.97, indicating good reliability for both.ConclusionLevator ani hiatus volume measurements performed using virtual reality were reliable and the results were similar to those obtained with conventional 3D ultrasonography. Copyright © 2012 ISUOG. Published by John Wiley & Sons, Ltd.
Gestational age at cervical length measurement and preterm birth in twins
Authors: Ehsanipoor R. M. , Haydon M. L. , Lyons Gaffaney C. , Jolley J. A. , Petersen R. , Lagrew D. C. , Wing D. A. 
Published: November 2011

AbstractObjectivesTo estimate the risk of preterm delivery of twin pregnancies based upon sonographic cervical length measurement and gestational age at measurement.MethodsTwin pregnancies that delivered between 1999 and 2005 and that underwent sonographic measurement of cervical length between 13 and 34 + 6 weeks' gestation were identified and a retrospective review performed. Women with anomalous pregnancies, multifetal reduction, cerclage placement or medically indicated deliveries before 35 weeks were excluded. Logistic regression analysis was used to estimate the risk of preterm delivery before 35 weeks.ResultsA total of 561 women underwent 2975 sonographic cervical length measurements during the study period. The rate of preterm delivery before 35 weeks was 19.4%. The risk of delivery before 35 weeks decreased by approximately 5% for each additional mm of cervical length (odds ratio (OR) 0.95 (95% CI, 0.93–0.97); P < 0.001) and by approximately 6% for each additional week at which the cervical length was measured (OR 0.94 (95% CI, 0.92–0.96); P < 0.001).ConclusionThe gestational age at which cervical length is measured is an important consideration when estimating the risk of spontaneous preterm birth in twins. The risk of preterm delivery is increased at earlier gestational ages and as cervical length decreases. Copyright © 2012 ISUOG. Published by John Wiley & Sons, Ltd.