bluuebunny/crossref_metadata_2025 huggingface dataset:
Directional asymmetry in the limbs, skull and pelvis of the silver fox (V. vulpes)
Authors: Kharlamova Anastasia V. , Trut Lyudmila N. , Chase Kevin , Kukekova Anna V. , Lark Karl G.
Published: September 2010

Directional asymmetry (DA) is a characteristic of most vertebrates, most strikingly exhibited by the placement of various organs (heart, lungs, liver, etc.) but also noted in small differences in the metrics of skeletal structures such as the pelvis of certain fish or sauropsids. We have analyzed DA in the skeleton of the fox (V. vulpes), using ∼1,000 radiographs of foxes from populations used in the genetic analysis of behavior and morphology. Careful measurements from this robust data base demonstrate that: 1) DA occurs in the limb bones, the ileum, and ischium and in the mandible; 2) regardless of the direction of the length asymmetry vector of a particular skeletal unit, the vectorial direction of length is always opposite to that of width; 3) with the exception of the humerus and radius, there is no correlation or inverse correlation between vectorial amplitudes or magnitudes of bone asymmetries. 4) Postnatal measurements on foxes demonstrate that the asymmetry increases after birth and continues to change (increasing or decreasing) during postnatal growth. 5) A behavior test for preferential use of a specific forelimb exhibited fluctuating asymmetry but not DA. None of the skeletal asymmetries were significantly correlated with a preferential use of a specific forelimb. We suggest that for the majority of fox skeletal parameters, growth on the right and left side of the fox are differentially biased resulting in fixed differences between the two sides in either the rate of growth or the length of the period during which growth occurs. Random effects around these fixed differences perturb the magnitude of the effects such that the magnitudes of length and width asymmetries are not inversely correlated at the level of individual animals. J. Morphol., 2010. © 2010 Wiley‐Liss, Inc.
A comparison of nine monthly air–sea flux products
Authors: Smith Shawn R. , Hughes Paul J. , Bourassa Mark A.
Published: September 2010

A comparison is conducted between nine monthly turbulent air–sea flux products. The analysis includes in situ‐based (Florida State University fluxes, FSU3 and National Oceanography Centre, NOC), satellite‐based (Hamburg Ocean‐Atmosphere Parameters from Satellite data, HOAPS2 and the French Research Institute for Exploitation of the Sea, IFREMER), hybrid (Goddard Satellite‐based Surface Turbulent Fluxes, GSSTF2 and objectively analysed fluxes, OAFLUX), and reanalysis (National Centers for Environmental Prediction, NCEPR2, Japanese 25‐year reanalysis, JRA, and European Centre for Medium Range Weather Forecasts reanalysis, ERA‐40) products. Objectives include documenting the varying analysis methodologies and quantifying the differences and similarities between the nine products. Recommendations are made for developers of future flux products and to guide users to select products most suitable for their application.

The comparison examines turbulent fluxes of heat and momentum along with the forcing variables (air temperature, wind speed, humidity, and ocean skin temperature) that are necessary to estimate turbulent fluxes. The wide range of turbulent flux parameterisations, sampling patterns, and averaging techniques within the products are described, including some of the difficulties product differences pose when trying to compare or apply the individual products. Global comparisons of monthly means tend to reveal similar spatial patterns in latent heat flux (LHF) and sensible heat flux (SHF) for the nine products; however, the magnitudes and patterns of variability (expressed as maps of standard deviations) are widely different. Basin scale and regional analysis further reveals large differences in the products (in some cases the interquartile ranges (IQRs) do not overlap for different products), but also reveals potential sources of the differences. For example, some of the variations in LHF can be explained by large differences in the distribution of specific humidity between the products. As a final analysis, we examine how each product represents the variations in turbulent fluxes in the equatorial Pacific (EP) Ocean. This analysis provides an example of how the choice of a flux product, and understanding the strengths and weaknesses of that product, can alter research findings. Copyright © 2010 Royal Meteorological Society
Isometric composition operators on the weighted Hardy spaces
Authors: Jaoua Nizar
Published: September 2010

We investigate the composition operators on the weighted Hardy spaces H2(β). For any bounded weight sequence β, we give necessary conditions for those operators to be isometric. The sufficiency of those conditions is well‐known for the classical space H2. In the case where β is non‐decreasing or non‐increasing, their sufficiency holds only for very few weighted spaces. We find out such spaces by characterizing the isometric monomial composition operators, first for a general β, then for any β as before. With no restriction on β, we provide a complete description of all isometric composition operators. We also prove that the unitary monomial ones are the same as those acting on H2. Such a fact extends to general symbols in the case where β is bounded (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On second order weakly hyperbolic equations with oscillating coefficients and regularity loss of the solutions
Authors: Hirosawa Fumihiko
Published: September 2010

Regularity of the solution for the wave equation with constant propagation speed is conserved with respect to time, but such a property is not true in general if the propagation speed is variable with respect to time. The main purpose of this paper is to describe the order of regularity loss of the solution due to the variable coefficient by the following four properties of the coefficient: “smoothness”, “oscillations”, “degeneration” and “stabilization”. Actually, we prove the Gevrey and C∞ well‐posedness for the wave equations with degenerate coefficients taking into account the interactions of these four properties. Moreover, we prove optimality of these results by constructing some examples (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Blowup phenomena for a new periodic nonlinearly dispersive wave equation
Authors: Hu Qiaoyi , Yin Zhaoyang
Published: September 2010

We first establish the local well‐posedness for a new periodic nonlinearly dispersive wave equation. We then present a precise blowup scenario and several blowup results of strong solutions to the equation. The obtained blowup results on the equation improve considerably recent results on the Camassa‐Holm equation and the rod equation (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On the completeness of the generalized eigenfunctions of elliptic operators on manifolds with conical singularities
Authors: Krainer Thomas
Published: September 2010

We show the completeness of the system of generalized eigenfunctions of closed extensions of elliptic cone operators under suitable conditions on the symbols (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
In vivo observation of intracellular oximetry in perfluorocarbon‐labeled glioma cells and chemotherapeutic response in the CNS using fluorine‐19 MRI
Authors: Kadayakkara Deepak K. K. , Janjic Jelena M. , Pusateri Lisa K. , Young Won‐Bin , Ahrens Eric T.
Published: September 2010

Preclinical development of therapeutic agents against cancer could greatly benefit from noninvasive markers of tumor killing. Potentially, the intracellular partial pressure of oxygen (pO2) can be used as an early marker of antitumor efficacy. Here, the feasibility of measuring intracellular pO2 of central nervous system glioma cells in vivo using 19F magnetic resonance techniques is examined. Rat 9L glioma cells were labeled with perfluoro‐15‐crown‐5‐ether ex vivo and then implanted into the rat striatum. 19F MRI was used to visualize tumor location in vivo. The mean 19F T1 of the implanted cells was measured using localized, single‐voxel spectroscopy. The intracellular pO2 in tumor cells was determined from an in vitro calibration curve. The basal pO2 of 9L cells (day 3) was determined to be 45.3 ± 5 mmHg (n = 6). Rats were then treated with a 1× LD10 dose of bischloroethylnitrosourea intravenously and changes in intracellular pO2 were monitored. The pO2 increased significantly (P = 0.042, paired T‐test) to 141.8 ± 3 mmHg within 18 h after bischloroethylnitrosourea treatment (day 4) and remained elevated (165 ± 24 mmHg) for at least 72 h (day 6). Intracellular localization of the perfluoro‐15‐crown‐5‐ether emulsion in 9L cells before and after bischloroethylnitrosourea treatment was confirmed by histological examination and fluorescence microscopy. Overall, noninvasive 19F magnetic resonance techniques may provide a valuable preclinical tool for monitoring therapeutic response against central nervous system or other deep‐seated tumors. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Brain MR perfusion‐weighted imaging with alternate ascending/descending directional navigation
Authors: Park Sung‐Hong , Duong Timothy Q.
Published: September 2010

In this study, a new arterial spin labeling technique that requires no separate spin preparation pulse was developed. Sequential two‐dimensional slices were acquired in ascending and descending orders by turns using balanced steady state free precession for pair‐wise subtraction. Simulation studies showed this new technique, alternate ascending/descending directional navigation (ALADDIN), has high sensitivity to both slow‐ (1–10 cm/sec) and fast‐moving (>10 cm/sec) blood because of the presence of multiple labeling planes proximal to imaging planes and sensitivity of balanced steady state free precession to initial magnetization differences. ALADDIN provided high‐resolution multislice perfusion‐weighted images in ∼3 min. About 80–90% of signals in a slice were ascribed to spins saturated in the four prior slices. Three to five edge slices on each side of imaging group were affected by transient magnetization transfer effects and incomplete T1 recovery between successive acquisitions. ALADDIN signals were dependent on many imaging parameters, implying room for improvement. Sagittal and coronal ALADDIN images demonstrated perfusion direction in gray matter regions was mostly from center to lateral, anterior, or posterior, whereas that in some white matter regions was reversed. ALADDIN is likely useful for many studies requiring perfusion‐weighted imaging with short scan time, insensitiveness to arterial transit time, directional information, high resolution, and/or wide coverage. Magn Reson Med, 2011. © 2010 Wiley‐Liss, Inc.
Longitudinal MR assessment of hypoxic ischemic injury in the immature rat brain
Authors: van de Looij Yohan , Chatagner Alexandra , Hüppi Petra S. , Gruetter Rolf , Sizonenko Stéphane V.
Published: September 2010

Extremely preterm infants commonly show brain injury with long‐term structural and functional consequences. Three‐day‐old (P3) rat pups share some similarities in terms of cerebral development with the very preterm infant (born at 24–28 weeks of gestation). The aim of this study was to assess longitudinally the cerebral structural and metabolic changes resulting from a moderate neonatal hypoxic ischemic injury in the P3 rat pup using high‐field (9.4 T) MRI and localized 1H magnetic resonance spectroscopy techniques. The rats were scanned longitudinally at P3, P4, P11, and P25. Volumetric measurements showed that the percentage of cortical loss in the long term correlated with size of damage 6 h after hypoxia–ischemia, male pups being more affected than female. The neurochemical profiles revealed an acute decrease of most of metabolite concentrations and an increase in lactate 24 h after hypoxia–ischemia, followed by a recovery phase leading to minor metabolic changes at P25 in spite of an abnormal brain development. Further, the increase of lactate concentration at P4 correlated with the cortical loss at P25, giving insight into the early prediction of long‐term cerebral alterations following a moderate hypoxia–ischemia insult that could be of interest in clinical practice. Magn Reson Med, 2011. © 2010 Wiley‐Liss, Inc.
An analytical description of balanced steady‐state free precession with finite radio‐frequency excitation
Authors: Bieri Oliver
Published: September 2010

Conceptually, the only flaw in the standard steady‐state free precession theory is the assumption of quasi‐instantaneous radio‐frequency pulses, and 10–20% signal deviations from theory are observed for common balanced steady‐state free precession protocols. This discrepancy in the steady‐state signal can be resolved by a simple T2 substitution taking into account reduced transverse relaxation effects during finite radio‐frequency excitation. However, finite radio‐frequency effects may also affect the transient phase of balanced steady‐state free precession, its contrast or its spin‐echo nature and thereby have an adverse effect on common steady‐state free precession magnetization preparation methods. As a result, an in‐depth understanding of finite radio‐frequency effects is not only of fundamental theoretical interest but also has direct practical implications. In this article, an analytical solution for balanced steady‐state free precession with finite radio‐frequency pulses is derived for the transient phase (under ideal conditions) and in the steady state demonstrating that balanced steady‐state free precession key features are preserved but revealing an unexpected dependency of finite radio‐frequency effects on relaxation times for the transient decay. Finally, the mathematical framework reveals that finite radio‐frequency theory can be understood as a generalization of alternating repetition time and fluctuating equilibrium steady‐state free precession sequence schemes. Magn Reson Med, 2011. © 2010 Wiley‐Liss, Inc.
Quantitative dynamic nuclear polarization‐NMR on blood plasma for assays of drug metabolism
Authors: Lerche Mathilde H. , Meier Sebastian , Jensen Pernille R. , Hustvedt Svein‐Olaf , Karlsson Magnus , Duus Jens Ø. , Ardenkjær‐Larsen Jan H.
Published: September 2010

Analytical platforms for the fast detection, identification and quantification of circulating drugs with a narrow therapeutic range are vital in clinical pharmacology. As a result of low drug concentrations, analytical tools need to provide high sensitivity and specificity. Dynamic nuclear polarization‐NMR (DNP‐NMR) in the form of the hyperpolarization–dissolution method should afford the sensitivity and spectral resolution for the direct detection and quantification of numerous isotopically labeled circulating drugs and their metabolites in single liquid‐state NMR transients. This study explores the capability of quantitativein vitroDNP‐NMR to assay drug metabolites in blood plasma. The lower limit of detection for the anti‐epileptic drug13C‐carbamazepine and its pharmacologically active metabolite13C‐carbamazepine‐10,11‐epoxide is 0.08 µg/mL in rabbit blood plasma analyzed by single‐scan13C DNP‐NMR. An internal standard is used for the accurate quantification of drug and metabolite. Comparison of quantitative DNP‐NMR data with an established analytical method (liquid chromatography‐mass spectrometry) yields a Pearson correlation coefficientrof 0.99. Notably, all DNP‐NMR determinations were performed without analyte derivatization or sample purification other than plasma protein precipitation. Quantitative DNP‐NMR is an emerging methodology which requires little sample preparation and yields quantitative data with high sensitivity for therapeutic drug monitoring. Copyright © 2010 John Wiley & Sons, Ltd.
Blood flow quantification of the human retina with MRI
Authors: Maleki Nasim , Dai Weiying , Alsop David C.
Published: September 2010

The purpose of this study was to investigate the feasibility of measuring blood flow to the retina using arterial spin labeling MRI, a quantitative, noninvasive tomographic technique. Blood flow imaging was performed in a single axial slice through both eyes of five healthy volunteers with no history of retinal diseases. The imaging was optimized to minimize the errors from motion and nonuniform magnetic fields caused by proximity to the sinuses. Key hemodynamic factors for flow quantification, including arterial transit delay and the apparent decay time of the signal, were estimated by repeated measurements with different arterial spin labeling timing. A clearly elevated signal, consistent with the anatomical location of the retina, was observed in all subjects. The measured blood flow to a 1 cm × 1.47 cm section of the retina, centered on the fovea, was 1.75 ± 0.54 µL/mm2/min (total blood flow of 261 ± 87 µL/min). The arterial transit delay from a labeling plane 5 cm below the slice was 1137 ± 288 ms. These results establish the feasibility of measuring blood flow to the retina with MRI, and support the future characterization of the healthy and diseased ocular circulation with this method. Copyright © 2010 John Wiley & Sons, Ltd.
Clinical characteristics and biomarkers of breast cancer associated with choline concentration measured by 1H MRS
Authors: Chen J.‐H. , Mehta R.S. , Baek H.‐M. , Nie K. , Liu H. , Lin M.Q. , Yu H.J. , Nalcioglu O. , Su M.‐Y.
Published: September 2010

This study investigated the association between the total choline (tCho) concentration and the clinical characteristics and biomarker status of breast cancer. Sixty‐two patients with breast cancer, 1.5 cm or larger in size on MR images, were studied. The tCho concentration was correlated with the MRI features, contrast enhancement kinetics, clinical variables and biomarkers. Pairwise two‐tailed Spearman's nonparametric test was used for statistical analysis. The tCho concentration was higher in high‐grade than moderate‐/low‐grade tumors (p = 0.04) and in tumors with higher Ktrans and kep (p < 0.001 for both). The association of tCho concentration with age (p = 0.05) and triple negative biomarker (p = 0.09) approached significance. tCho was not detected in 17 patients, including 15 with invasive ductal cancer and two with infiltrating lobular cancer. Fifteen of the 17 patients had moderate‐ to low‐grade cancers, and 11 had human epidermal growth factor‐2‐negative cancer, suggesting that these two factors might lead to false‐negative choline. Higher tCho concentration in high‐grade tumors and tumors with higher Ktrans and kep indicates that choline is associated with cell proliferation and tumor angiogenesis. The higher choline level in younger women may be caused by their more aggressive tumor type. The results presented here may aid in the better interpretation of 1H MRS for the diagnosis of breast lesions. Copyright © 2010 John Wiley & Sons, Ltd.
Fast, reproducible measurement of the vascular input function in mice using constrained reconstruction and cardiac sampling
Authors: Ragan Dustin K. , Lai Stephen Y. , Bankson James A.
Published: September 2010

Dynamic contrast‐enhanced MRI is often used to assess the response to therapy in small animal models of cancer. Rigorous quantification of dynamic contrast‐enhanced MRI data using common pharmacokinetic models requires dynamic determination of the concentration of contrast in tumor tissue and in blood. Measurement of the blood concentration, or vascular input function (VIF), requires high temporal resolution and is prone to distortion as a result of flow and partial volume artifacts when measured in local blood vessels. We have developed a strategy for the robust measurement of VIF in mice that uses a constrained reconstruction algorithm to enable sampling from the left ventricle of the heart. The feasibility of the algorithm and its resistance to cardiac motion are demonstrated in vivo and through numerical simulations. VIF sampling is interleaved with slices dedicated to tumor coverage to yield a fast VIF sampling period (81 ms) that is decoupled from the temporal resolution of tumor data (3.9 s). The algorithm provides results that agree with fully encoded measurements in the slowly varying component of VIF to within a 4% root‐mean‐square signal difference. Analysis of a parametric representation of VIFs measured in a population of mice showed a significant reduction in variations observed within subjects (5%–58% over four parameters; p < 0.05) and a reduction in variations between subjects (19%–62%) when using this technique. Preliminary dynamic measurements in an orthotopic xenograft model of anaplastic thyroid cancer revealed a decrease in the variation of pharmacokinetic parameters between mice by a factor of two. Copyright © 2010 John Wiley & Sons, Ltd.
Surface modification of spruce wood flour and effects on the dynamic fragility of PLA/wood composites
Authors: Gregorova Adriana , Hrabalova Marta , Kovalcik Rene , Wimmer Rupert
Published: September 2010

Poly (lactic acid) (PLA), a biodegradable aliphatic semicrystalline polyester was filled with 40 wt% spruce wood flour (WF), to produce composite materials. Hydrothermal treatment, as well as maleic anhydride, vinyltrimethoxysilane, and stearic acid surface treatments were applied. The influence of surface modifications for WF was tested in terms of thermal, mechanical, and viscoelastic properties. The recorded results show that in both, the untreated and treated PLA/WF composites, the rigid amorphous phase content has been enhanced. The presence of WF causes a stiffness increase of the PLA/WF composites, while damping factor was decreased. The effect of wood surface modifications on interfacial compatibility with PLA was estimated by dynamic fragility parameter m calculated according the Williams‐Landel‐Ferry equation. The incorporation of untreated WF increased dynamic fragility of PLA/WF composites markedly, whereas used silane, maleic anhydride and hydrothermal treatments lead to lower values of parameter m. POLYM. ENG. SCI., 2011. © 2010 Society of Plastics Engineers
Producing continuous twisted yarn from well‐aligned nanofibers by water vortex
Authors: Yousefzadeh Maryam , Latifi Masoud , Teo Wee‐Eong , Amani‐Tehran Mohammad , Ramakrishna Seeram
Published: September 2010

A new technology based on the liquid support system is introduced for fabricating continuous twisted nanofibrous yarn. In this novel technique, the electrospun yarn was collected from the top of the water vortex such that it can be twisted simultaneously during yarn production. Our study demonstrated the feasibility of the technique for producing continuous twisted yarn from well aligned nanofibers. It is shown that the system can be modified to have different yarn counts with various twists. Further, significant improvement can be seen in the strength and strain when nanofibrous yarn is twisted compared to non‐twisted yarn. POLYM. ENG. SCI., 2011. © 2010 Society of Plastics Engineers
A Device for Testing Thermal Impact Sensitivity of High Explosives
Authors: Zhang Gengxin , Weeks Brandon L.
Published: September 2010

A drop‐weight instrument is described to investigate the impact sensitivity of high explosives at elevated temperatures. This test is typically performed to discover potential safety aspects of either newly synthesized materials of unknown behavior. Normally, drop‐weight impact sensitivity tests are conducted at room temperature, since high explosives are often stored or handled at room temperature. The instrument described here has the capability of heating the samples from ambient to 300 °C prior to impact. The thermal impact sensitivities of PETN, TATP, HMX, and silver azide (AgN3) as a function of temperature are obtained. The phase transition of HMX can clearly be observed by a significant decrease in the impact height in situ.
Automated minimization of steric clashes in protein structures
Authors: Ramachandran Srinivas , Kota Pradeep , Ding Feng , Dokholyan Nikolay V.
Published: September 2010

Molecular modeling of proteins including homology modeling, structure determination, and knowledge‐based protein design requires tools to evaluate and refine three‐dimensional protein structures. Steric clash is one of the artifacts prevalent in low‐resolution structures and homology models. Steric clashes arise due to the unnatural overlap of any two nonbonding atoms in a protein structure. Usually, removal of severe steric clashes in some structures is challenging since many existing refinement programs do not accept structures with severe steric clashes. Here, we present a quantitative approach of identifying steric clashes in proteins by defining clashes based on the Van der Waals repulsion energy of the clashing atoms. We also define a metric for quantitative estimation of the severity of clashes in proteins by performing statistical analysis of clashes in high‐resolution protein structures. We describe a rapid, automated, and robust protocol, Chiron, which efficiently resolves severe clashes in low‐resolution structures and homology models with minimal perturbation in the protein backbone. Benchmark studies highlight the efficiency and robustness of Chiron compared with other widely used methods. We provide Chiron as an automated web server to evaluate and resolve clashes in protein structures that can be further used for more accurate protein design. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Exploring coumarin egress channels in human cytochrome p450 2a6 by random acceleration and steered molecular dynamics simulations
Authors: Li Weihua , Shen Jie , Liu Guixia , Tang Yun , Hoshino Tyuji
Published: September 2010

The kinetic analysis of coumarin oxidation by CYP2A6 suggested that substrate binding and release occurred in the multiple steps and such events proceeded rapidly. However, the crystal structure of the CYP2A6‐coumarin complex reveals that no obvious channel is open enough to allow coumarin to pass through. Thus, an intriguing and important question arises: how coumarin enters and exits the active site, which is deeply buried at the center of CYP2A6 fold. In this study, geometric analysis of the potential openings was first performed on all the available crystal structures of CYP2A6. And then, random acceleration molecular dynamics simulations were used to explore the possible substrate egress channels in CYP2A6. Two channels were most frequently observed. Afterwards, steered molecular dynamics simulations were performed and potentials of mean force were constructed to compare the preference of the two channels serving as the substrate egress channel. The results showed that channel 2c, which is located between helices I and G and the helix B'‐C region, was the most likely channel for coumarin egress. The opening of channel 2c was characterized by a rotation of Phe111 together with a bending of helix B'. Our findings will not only be helpful for understanding the unbinding mechanism of coumarin and for identifying structural determinants related to the biological function of CYP2A6, but also provide further insight into the channel selectivity of P450s. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Theoretical study of NMR chemical shift induced by H/D isotope effect
Authors: Sugimori Kimikazu , Kawabe Hiroyuki
Published: September 2010

The isotope effect induced by deuterium substituted species is observed in molecular properties, such as geometry, kinetics, and electronic state, of the molecules through nuclear‐electron interaction. Theoretical considerations and experimental alignments have been studied by ab initio molecular orbital, density functional theory, and other empirical strategies. The Born‐Oppenheimer approximation with nuclear vibrational wavefunction can treat isotope effect because nuclear mass effect account for the average distance of vibrational motion. In this study, we introduce Morse anharmonic oscillator model to calculate average internuclear distance of diatomic molecules having X‐H bonding and X‐D bonding. Morse parameters are determined by fitting to potential energy surface of molecular orbital and/or density functional calculations, and then the average distance are obtained as the expectation value of the analytical Morse vibrational wavefunction. Nuclear magnetic resonance shielding constants of the H/D isotopomer are calculated again on the average distance by using GIAO with B3LYP and CCSD calculation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Highly sensitive localization analysis of gangliosides and sulfatides including structural isomers in mouse cerebellum sections by combination of laser microdissection and hydrophilic interaction liquid chromatography/electrospray ionization mass spectrometry with theoretically expanded multiple reaction monitoring
Authors: Ikeda Kazutaka , Taguchi Ryo
Published: September 2010

Liquid chromatography/electrospray ionization mass spectrometry (LC/ESI‐MS) is suitable for analysis of glycosphingolipids such as fragile gangliosides avoiding the use of the sialic acid elimination. However, it was not possible to distinguish the structural isomers such as GD1a and GD1b with reversed‐phase LC/ESI‐MS by hydrophobic interaction. Here we report an effective method for targeted analysis of theoretically expanded ganglioside molecular species including structural isomers by hydrophilic interaction liquid chromatography (HILIC)/ESI‐MS with multiple reaction monitoring (MRM). As a result of MRM analysis of glycosphingolipid mixtures from porcine brain, each of the lipid classes was detected within 25 min in the following order: sulfatides > GM3 > GM2 > GM1 > GD3 > GD1a > GD2 > GD1b > GT1a > GT1b > GQ1b. For the advanced application, localization analysis of postnatal day 15 (P15) mouse cerebellum layered structures was carried out by combination of MRM and laser microdissection (LMD). As a result, GM3, GD1a, GT1b and GQ1b were abundantly detected in the molecular and granular layers, whereas GM1 was widely presented in each layered structure. These gangliosides were mainly composed of d18:1‐18:0 and d18:1‐20:0, but GM3 was d18:1‐16:0 and d18:1‐20:0. Meanwhile, sulfatide molecular species were mostly localized in the myelinated fibers and scarcely found in the molecular layer. These results suggested that our method is suitable to detect a variety of ganglioside classes and sulfatides with high sensitivity at the molecular species level and effective for localization analysis of these glycosphingolipids from mouse brain sections. Copyright © 2010 John Wiley & Sons, Ltd.
Elucidation of the decomposition pathways of protonated and deprotonated estrone ions: application to the identification of photolysis products
Authors: Bourcier Sophie , Poisson Clémentine , Souissi Yasmine , Kinani Said , Bouchonnet Stéphane , Sablier Michel
Published: September 2010

With the future aim of elucidating the unknown structures of estrogen degradation products, we characterized the dissociation pathways of protonated estrone (E1) under collisional activation in liquid chromatography/tandem mass spectrometry (LC/MS/MS) experiments employing a quadrupole time‐of‐flight mass spectrometer. Positive ion and negative ion modes give information on the protonated and deprotonated molecules and their product ions. The mass spectra of estrone methyl ether (CH3‐E1) and estrone‐d4 (E1‐d4) were compared with that of E1 in order (i) to elucidate the dissociation mechanisms of protonated and deprotonated molecules and (ii) to propose likely structures for each product ions. The positive ion acquisition mode yielded more fragmentation. The mass spectra of E1 were compared with those of estradiol (E2), estriol (E3) and 17‐ethynylestradiol (EE2). This comparison allowed the identification of marker ions for each ring of the estrogenic structure. Accurate mass measurements have been carried out for all the identified ions. The resulting ions revealed to be useful for the characterization of structural modifications induced by photolysis on each ring of the estrone molecule. These results are very promising for the determination of new metabolites in the environment. Copyright © 2010 John Wiley & Sons, Ltd.
Food contaminant analysis at ultra‐high mass resolution: application of hybrid linear ion trap – orbitrap mass spectrometry for the determination of the polyether toxins, azaspiracids, in shellfish
Authors: Škrabáková Zuzana , O'Halloran John , van Pelt Frank N.A.M. , James Kevin J.
Published: September 2010

The biotoxins, azaspiracids (AZAs), from marine phytoplankton accumulate in shellfish and affect human health by causing severe gastrointestinal disturbance, diarrhea, nausea and vomiting. Specific and sensitive methods have been developed and validated for the determination of the most commonly occurring azaspiracid analogs. An LTQ Orbitrap mass spectrometer is a hybrid instrument that combines linear ion trap (LIT) mass spectrometry (MS) with high‐resolution Fourier transform (FT) MS and this was exploited to perform simultaneous ultra‐high‐resolution full‐scan MS analysis and collision‐induced dissociation (CID) tandem mass spectrometry (MS/MS). Using the highest mass resolution setting (100 000 FWHM) in full‐scan mode, the methodology was validated for the determination of six AZAs in mussel (Mytilus galloprovincialis) tissue extracts. Ultra‐high mass resolution, together with a narrow mass tolerance window of ±2 mDa, dramatically improved detection sensitivity. In addition to employing chromatographic resolution to distinguish between the isomeric azaspiracid analogs, AZA1/AZA6 and AZA4/AZA5, higher energy collisionally induced dissociation (HCD) fragmentation on selected precursor ions were performed in parallel with full‐scan FTMS. Using HCD MS/MS, most precursor and product ion masses were determined within 1 ppm of the theoretical m/z values throughout the mass spectral range and this enhanced the reliability of analyte identity.

For the analysis of mussels (M. galloprovincialis), the method limit of quantitation (LOQ) was 0.010 µg/g using full‐scan FTMS and this was comparable with the LOQ (0.007 µg/g) using CID MS/MS. The repeatability data were; intra‐day RSD% (1.8–4.4%; n = 6) and inter‐day RSD% (4.7–8.6%; n = 3). Application of these methods to the analysis of mussels (M. edulis) that were naturally contaminated with azaspiracids, using high‐resolution full‐scan Orbitrap MS and low‐resolution CID MS/MS, produced equivalent quantitative data. Copyright © 2010 John Wiley & Sons, Ltd.
Geographic origin of southern Brazilian wines by carbon and oxygen isotope analyses
Authors: Adami Laurien , Dutra Sandra Valduga , Marcon Ângela Rossi , Carnieli Gilberto João , Roani Carlos André , Vanderlinde Regina
Published: September 2010

We present a method that can differentiate between the varieties of grapes and the vintages of wines and show the relationship between the grapes, the wine and the geographic location. The place of origin and its geographic and climatic characteristics were determined by the isotopic ratios, 13C/12C of the ethanol and 18O/16O of the water content of wine (wine water), for southern Brazil wines. The producing subregions of Pinto Bandeira, Vale dos Vinhedos and Nova Pádua showed differences in the temperature, rainfall and humidity conditions used for the production under microvinification conditions of Merlot and Cabernet Sauvignon varieties, in the harvests of 2005 and 2006. An isotope ratio mass spectrometer coupled to an elemental analyzer was used to measure the 13C/12C of ethanol and the 18O/16O of wine water. Regardless of the grape variety used, it was possible to determine the subregion through measurement of the δ18O values in both harvests. The altitudes of the different subregions led to statistical differences and demonstrated an influence mainly on the δ18O values of wine water. The δ18O value of wine water was determined to be more selective for the determination of the cultivation subregions than the δ13C value of the ethanol. The altitude and latitude influenced mainly the δ 18O values of wine water and the ethanol. The climatic influences are more noteworthy in distinguishing the year of the harvest than the cultivation subregion. Copyright © 2010 John Wiley & Sons, Ltd.
Characterization and identification of saponins in Achyranthes bidentata by rapid‐resolution liquid chromatography with electrospray ionization quadrupole time‐of‐flight tandem mass spectrometry
Authors: Li Yan‐Jing , Wei Huan‐Li , Qi Lian‐Wen , Chen Jun , Ren Mei‐Ting , Li Ping
Published: September 2010

A rapid‐resolution liquid chromatography (RRLC) method coupled with electrospray ionization quadrupole time‐of‐flight tandem mass spectrometry (Q‐TOF MS/MS) has been developed for analysis of oleanane‐type triterpenoid saponins in Achyranthes bidentata. Collision‐induced dissociation techniques were used to fragment the precursor molecular ions and the resulting product ions. A retro‐Diels‐Alder rearrangement from the oleanane aglycone skeleton in the MS/MS process yielded characteristic fragment ions in positive ion mode. These characteristic ions were helpful in predicting the aglycone structure. Losses of monosaccharide sequences, presence of sugar‐chain fragment ions, and cleavage of CO2 were observed for important information on sugar types and attachment sequences. Fragmentation rules of three major groups of saponins from A. bidentata were summarized, and the possible fragmentation pathways were proposed. A total of 22 compounds including both the target and unknown oleanane‐type triterpenoid saponins were rapidly screened and predicted in the herbal extract by the developed method. The RRLC‐Q‐TOF MS/MS method has provided a powerful approach for rapid separation, target screening and structural elucidation of oleanane‐type saponins, and also opened perspectives for similar studies on other herbal medicines. Copyright © 2010 John Wiley & Sons, Ltd.
Determining the topology of virus assembly intermediates using ion mobility spectrometry–mass spectrometry
Authors: Knapman Tom W. , Morton Victoria L. , Stonehouse Nicola J. , Stockley Peter G. , Ashcroft Alison E.
Published: September 2010

We have combined ion mobility spectrometry–mass spectrometry with tandem mass spectrometry to characterise large, non‐covalently bound macromolecular complexes in terms of mass, shape (cross‐sectional area) and stability (dissociation) in a single experiment. The results indicate that the quaternary architecture of a complex influences its residual shape following removal of a single subunit by collision‐induced dissociation tandem mass spectrometry. Complexes whose subunits are bound to several neighbouring subunits to create a ring‐like three‐dimensional (3D) architecture undergo significant collapse upon dissociation. In contrast, subunits which have only a single neighbouring subunit within a complex retain much of their original shape upon complex dissociation. Specifically, we have determined the architecture of two transient, on‐pathway intermediates observed during in vitro viral capsid assembly. Knowledge of the mass, stoichiometry and cross‐sectional area of each viral assembly intermediate allowed us to model a range of potential structures based on the known X‐ray structure of the coat protein building blocks. Comparing the cross‐sectional areas of these potential architectures before and after dissociation provided tangible evidence for the assignment of the topologies of the complexes, which have been found to encompass both the 3‐fold and the 5‐fold symmetry axes of the final icosahedral viral shell. Such insights provide unique information about virus assembly pathways that could allow the design of anti‐viral therapeutics directed at the assembly step. This methodology can be readily applied to the structural characterisation of many other non‐covalently bound macromolecular complexes and their assembly pathways. Copyright © 2010 John Wiley & Sons, Ltd.
Quantification of deuterated bisphenol A in serum, tissues, and excreta from adult Sprague‐Dawley rats using liquid chromatography with tandem mass spectrometry
Authors: Twaddle Nathan C. , Churchwell Mona I. , Vanlandingham Michelle , Doerge Daniel R.
Published: September 2010

Bisphenol A (BPA) is an important industrial chemical used in the manufacture of polycarbonate plastic products, epoxy resin‐based food can liners, and paper products. The presence of BPA in urine of >90% of Americans aged 6–60 suggests ubiquitous and frequent exposure and is problematic because of the potential for endocrine disruption. The ubiquity of environmental BPA in common laboratory supplies used for sample collection, storage, and analysis greatly increases the likelihood of false positive determinations, particularly at trace levels. The current study validated using liquid chromatography/tandem mass spectrometry (LC/MS/MS) in conjunction with deuterated BPA as the dosing material to circumvent contamination for high sensitivity quantifications in rat serum, tissues, urine, and feces. The methods described provided measurements of both estrogen receptor‐active aglycone and metabolically deactivated conjugated forms of BPA, a distinction that is critical to assessing toxicological potential. The adequacy of the described methodology was substantiated by its utility in analyzing samples from rats treated orally with a 100 µg/kg body weight dose of d6‐BPA. These results emphasize the challenges inherent in measuring BPA in biological samples and how employing stable isotope labeled dosing can facilitate pharmacokinetic studies needed to understand BPA metabolism and disposition. Such studies conducted in experimental animal models, in conjunction with properly validated human biomonitoring data, will be the basis for PBPK modeling of BPA in environmentally exposed humans. Published in 2010 by John Wiley & Sons, Ltd.
High‐performance liquid chromatography/mass spectrometric and proton nuclear magnetic resonance spectroscopic studies of the transacylation and hydrolysis of the acyl glucuronides of a series of phenylacetic acids in buffer and human plasma
Authors: Karlsson Elin S. , Johnson Caroline H. , Sarda Sunil , Iddon Lisa , Iqbal Mazhar , Meng Xiaoli , Harding John R. , Stachulski Andrew V. , Nicholson Jeremy K. , Wilson Ian D. , Lindon John C.
Published: September 2010

The use of high‐performance liquid chromatography/mass spectrometry (HPLC/MS) and proton nuclear magnetic resonance (1H NMR) spectroscopy for the kinetic analysis of acyl glucuronide (AG) isomerisation and hydrolysis of the 1‐β‐O‐acyl glucuronides (1‐β‐O‐AG) of phenylacetic acid, (R)‐ and (S)‐α‐methylphenylacetic acid and α,α‐dimethylphenylacetic acid is described and compared. Each AG was incubated in both aqueous buffer, at pH 7.4, and control human plasma at 37°C. Aliquots of these incubations, taken throughout the reaction time‐course, were analysed by HPLC/MS and1H NMR spectroscopy. In buffer, transacylation reactions predominated, with relatively little hydrolysis to the free aglycone observed. In human plasma incubations the calculated rates of reaction were much faster than for buffer and, in contrast to the observations in buffer, hydrolysis to the free aglycone was a significant contributor to the overall reaction.

A diagnostic analytical methodology based on differential mass spectrometric fragmentation of 1‐β‐O‐AGs compared to the 2‐, 3‐ and 4‐positional isomers, which enables selective determination of the former, was confirmed and applied. These findings show that HPLC/MS offers a viable alternative to the more commonly used NMR spectroscopic approach for the determination of the transacylation and hydrolysis reactions of these AGs, with the major advantage of having the capability to do so in a complex biological matrix such as plasma. Copyright © 2010 John Wiley & Sons, Ltd.
Cure fraction model with random effects for regional variation in cancer survival
Authors: Seppä Karri , Hakulinen Timo , Kim Hyon‐Jung , Läärä Esa
Published: September 2010

Assessing regional differences in the survival of cancer patients is important but difficult when separate regions are small or sparsely populated. In this paper, we apply a mixture cure fraction model with random effects to cause‐specific survival data of female breast cancer patients collected by the population‐based Finnish Cancer Registry. Two sets of random effects were used to capture the regional variation in the cure fraction and in the survival of the non‐cured patients, respectively. This hierarchical model was implemented in a Bayesian framework using a Metropolis‐within‐Gibbs algorithm. To avoid poor mixing of the Markov chain, when the variance of either set of random effects was close to zero, posterior simulations were based on a parameter‐expanded model with tailor‐made proposal distributions in Metropolis steps. The random effects allowed the fitting of the cure fraction model to the sparse regional data and the estimation of the regional variation in 10‐year cause‐specific breast cancer survival with a parsimonious number of parameters. Before 1986, the capital of Finland clearly stood out from the rest, but since then all the 21 hospital districts have achieved approximately the same level of survival. Copyright © 2010 John Wiley & Sons, Ltd.
Using ancestry matching to combine family‐based and unrelated samples for genome‐wide association studies
Authors: Crossett Andrew , Kent Brian P. , Klei Lambertus , Ringquist Steven , Trucco Massimo , Roeder Kathryn , Devlin Bernie
Published: September 2010

We propose a method to analyze family‐based samples together with unrelated cases and controls. The method builds on the idea of matched case–control analysis using conditional logistic regression (CLR). For each trio within the family, a case (the proband) and matched pseudo‐controls are constructed, based upon the transmitted and untransmitted alleles. Unrelated controls, matched by genetic ancestry, supplement the sample of pseudo‐controls; likewise unrelated cases are also paired with genetically matched controls. Within each matched stratum, the case genotype is contrasted with control/pseudo‐control genotypes via CLR, using a method we call matched‐CLR (mCLR). Eigenanalysis of numerous SNP genotypes provides a tool for mapping genetic ancestry. The result of such an analysis can be thought of as a multidimensional map, or eigenmap, in which the relative genetic similarities and differences amongst individuals is encoded in the map. Once constructed, new individuals can be projected onto the ancestry map based on their genotypes. Successful differentiation of individuals of distinct ancestry depends on having a diverse, yet representative sample from which to construct the ancestry map. Once samples are well‐matched, mCLR yields comparable power to competing methods while ensuring excellent control over Type I error. Copyright © 2010 John Wiley & Sons, Ltd.