bluuebunny/crossref_metadata_2025 huggingface dataset:
Atomic forces for geometry‐dependent point multipole and Gaussian multipole models
Authors: Elking Dennis M. , Perera Lalith , Duke Robert , Darden Thomas , Pedersen Lee G.
Published: May 2010

In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise because of (1) the transfer of torque between neighboring atoms and (2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry‐dependent multipole models. In this study, atomic force expressions for geometry‐dependent multipoles are presented for use in simulations of flexible molecules. The atomic forces are derived by first proposing a new general expression for Wigner function derivatives $\partial D_{m'm}^l /\partial \Omega$. The force equations can be applied to electrostatic models based on atomic point multipoles or Gaussian multipole charge density. Hydrogen‐bonded dimers are used to test the intermolecular electrostatic energies and atomic forces calculated by geometry‐dependent multipoles fit to the ab initio electrostatic potential. The electrostatic energies and forces are compared with their reference ab initio values. It is shown that both static and geometry‐dependent multipole models are able to reproduce total molecular forces and torques with respect to ab initio, whereas geometry‐dependent multipoles are needed to reproduce ab initio atomic forces. The expressions for atomic force can be used in simulations of flexible molecules with atomic multipoles. In addition, the results presented in this work should lead to further development of next generation force fields composed of geometry‐dependent multipole models. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010
Docetaxel increases antitumor efficacy of oncolytic prostate‐restricted replicative adenovirus by enhancing cell killing and virus distribution
Authors: Li Xiong , Liu Youhong , Tang Yong , Roger Phipps , Jeng Meei‐Huey , Kao Chinghai
Published: May 2010

Background

We explored multiple molecular mechanisms of the combination of docetaxel and an oncolytic prostate‐restricted replication competent adenovirus (Ad) (PRRA) in advanced prostate cancer (PCa) models. The combinational therapy has potential to overcome the therapeutic limitations of poor virus distribution inside solid tumors.

Methods

We evaluated the effect of docetaxel on the antitumor efficacy and efficiency of virus transduction, transgene expression and virus distribution of PRRA in a prostate‐specific antigen/prostate‐specific membrane antigen‐positive tumor xenograft model. We also evaluated the effect of docetaxel on apoptosis induction, cell killing and the efficiency of transgene expression and virus replication in vitro.

Results

Tumor growth inhibition was significantly enhanced when docetaxel was administrated before intratumor injection of PRRA. In vivo dual‐photon microscopy and ex vivo fluorescence microscopy and immunohistochemistry showed that docetaxel increased transgene expression and expanded virus distribution. The combination of docetaxel and PRRA also increased cell apoptosis. In vitro, docetaxel significantly increased cell killing in PRRA‐treated PCa cells. Docetaxel significantly increased Ad‐mediated trangene expression independent of Ad binding receptors and replication capability. Docetaxel increased the activity of cytomegalovirus (CMV) promoter but not of a chimeric prostate‐specific enhancer, resulting in higher transgene expression. The enhanced CMV promoter activity resulted from activation of p38 mitogen‐activated protein kinase (MAPK) because inhibition of p38 MAPK blocked the docetaxel‐induced increase in CMV promoter activity.

Conclusions

Combining docetaxel with an oncolytic PRRA improved therapeutic potential by expanding virus distribution and enhancing cell apoptosis and killing. These studies suggested a novel mechanism for enhancing the effect of therapeutic genes delivered by a PRRA. Copyright © 2010 John Wiley & Sons, Ltd.
LOCAL GOVERNMENT DISCRETION AND ACCOUNTABILITY IN PHILIPPINES
Authors: Yilmaz Serdar , Venugopal Varsha
Published: May 2010

Philippines has an exhaustive decentralisation code providing local governments with a high degree of discretion. But the concurrent upward and downward accountability mechanisms are weak resulting in inefficiency and ineffectiveness of local governments. We employ a diagnostic framework to analyse local governments' discretion and accountability in political, administrative and fiscal domains. We find that the entrenched culture of power accumulation and patronage—within which decentralisation operates—has resulted in elite capture at the local level. This along with lack of capacity at national and local levels has caused serious impediments in downward accountability of local governments. Copyright © 2010 John Wiley & Sons, Ltd.
New insights into the complex structure and ontogeny of the occipito‐vertebral gap in barbeled dragonfishes (Stomiidae, Teleostei)
Authors: Schnell Nalani K. , Britz Ralf , Johnson G. David
Published: May 2010

In all stomiid genera there is an occipito‐vertebral gap between the skull and the first vertebra bridged only by the flexible notochord. Morphological studies from the early 20th century suggested that some stomiid genera have 1–10 of the anteriormost centra reduced or entire vertebrae missing in this region. Our study reviews this previous hypothesis. Using a new approach, we show that only in Chauliodus, Eustomias and Leptostomias gladiator vertebral centra are actually lost, with their respective neural arches and parapophyses persisting. We present results from a comparative analysis of the number and insertion sites of the anteriormost myosepta in 26 of the 28 stomiid genera. Generally in teleosts the first three myosepta are associated with the occiput, and the fourth is the first vertebral myoseptum. The insertion site of the fourth myoseptum plays an important role in this analysis, because it provides a landmark for the first vertebra. Lack of association of the fourth myoseptum with a vertebra is thus evidence that the first vertebra is reduced or absent. By counting the occipital and vertebral myosepta the number of reduced vertebrae in Chauliodus, Eustomias and Leptostomias gladiator can be inferred. Proper identification of the spino‐occipital nerves provides an additional source of information about vertebral reduction. In all other stomiid genera the extensive occipito‐ vertebral gap is not a consequence of the reduction of vertebrae, but of an elongation of the notochord. The complex structure and ontogeny of the anterior part of the vertebral column of stomiids are discussed comparatively. J. Morphol. 271:1006–1022, 2010. © 2010 Wiley‐Liss, Inc.
Morphology and function of the hyoid apparatus of fossil xenarthrans (mammalia)
Authors: Pérez Leandro M. , Toledo Néstor , De Iuliis Gerardo , Bargo M. Susana , Vizcaíno Sergio F.
Published: May 2010

The analysis of the hyoid apparatus of fossil xenarthrans provides insight on the form of the tongue and its function in food intake and intraoral processing. The hyoid apparatus of xenarthrans is notable for fusion among its elements. The presence of a V‐bone, a complex consisting of fused basihyal and thyrohyal bones, is a consistent and probably synapomorphic feature of xenarthrans. Fusion of other elements is variable in fossil xenarthrans. Most fossil sloths retain independent elements, as in living dasypodids and mammals generally. Among nothrotheriids, the elements are slender and their articular surfaces indicate considerable mobility, and the relatively long and horizontal orientation of the geniohyoid muscle suggests considerable tongue protrusion. Among mylodontines, such as Paramylodon and Glossotherium, the elements indicate relatively mobile articulations, except between the stylo‐ and epihyals. The relatively posterior placement of the apparatus and the length and alignment of the geniohyoid muscle indicate considerable capacity for tongue protrusion. Scelidotherium, however, had rigidly articulated stylohyal and epihyal, and the apparatus lies farther anteriorly, which together with the elongated, steeply inclined mandibular symphysis, indicates a relatively shorter geniohyoid muscle and thus more limited capacity for tongue protrusion. A similar situation is indicated for Megatherium, casting doubt on the classical reconstruction of this sloth as having a long prehensile tongue. Among cingulates Prozaedyus resembles living dasypodids, indicating considerable tongue protrusion important in food acquisition and intake. More extensive fusion of hyoid elements occurs in the cingulates Glyptodon and Proeutatus, in which the stylohyal and epihyal at least, are fused into a single element termed the sigmohyal. The presence of this element supports recent proposals of a sister‐group relationship between glyptodonts and eutatines. The rigidity of the apparatus suggests limited tongue protrusion, but the tongue, in glyptodonts at least, was a powerful structure important for intraoral manipulation of food. J. Morphol. 271:1119–1133, 2010. © 2010 Wiley‐Liss, Inc.
Thermodynamic characterization of OsGID1‐gibberellin binding using calorimetry and docking simulations
Authors: Xiang Hongyu , Takeuchi Hiromi , Tsunoda Yuki , Nakajima Masatoshi , Murata Katsuyoshi , Ueguchi‐Tanaka Miyako , Kidokoro Shun‐ichi , Kezuka Yuichiro , Nonaka Takamasa , Matsuoka Makoto , Katoh Etsuko
Published: May 2010

Gibberellins (GAs) are phytohormones regulating various developmental processes in plants. In rice, the initial GA‐signaling events involve the binding of a GA to the soluble GA receptor protein, GID1. Although X‐ray structures for certain GID1/GA complexes have recently been determined, an examination of the complexes does not fully clarify how GID1s discriminate among different GAs. Herein, we present a study aimed at defining the types of forces important to binding via a combination of isothermal titration calorimetry (ITC) and computational docking studies that employed rice GID1 (OsGID1), OsGID1 mutants, which were designed to have a decreased possible number of hydrogen bonds with bound GA, and GA variants. We find that, in general, GA binding is enthalpically driven and that a hydrogen bond between the phenolic hydroxyl of OsGID1 Tyr134 and the C‐3 hydroxyl of a GA is a defining structural element. A hydrogen‐bond network that involves the C‐6 carboxyl of a GA that directly hydrogen bonds the hydroxyl of Ser198 and indirectly, via a two‐water‐molecule network, the phenolic hydroxyl of Tyr329 and the NH of the amide side‐chain of Asn255 is also important for GA binding. The binding of OsGID1 by GA1 is the most enthalpically driven association found for the biologically active GAs evaluated in this study. This observation might be a consequence of a hydrogen bond formed between the hydroxyl at the C‐13 position of GA1 and the main chain carbonyl of OsGID1 Phe245. Our results demonstrate that by combining ITC experiments and computational methods much can be learned about the thermodynamics of ligand/protein binding. Copyright © 2010 John Wiley & Sons, Ltd.
Positive chemical ionization triple‐quadrupole mass spectrometry and ab initio computational studies of the multi‐pathway fragmentation of phthalates
Authors: Jeilani Yassin A. , Cardelino Beatriz H. , Ibeanusi Victor M.
Published: May 2010

We report the first positive chemical ionization (PCI) fragmentation mechanisms of phthalates using triple‐quadrupole mass spectrometry and ab initio computational studies using density functional theories (DFT). Methane PCI spectra showed abundant [M + H]+, together with [M + C2H5]+ and [M + C3H5]+. Fragmentation of [M + H]+, [M + C2H5]+ and [M + C3H5]+ involved characteristic ions at m/z 149, 177 and 189, assigned as protonated phthalic anhydride and an adduct of phthalic anhydride with C2H5+ and C3H5+, respectively. Fragmentation of these ions provided more structural information from the PCI spectra. A multi‐pathway fragmentation was proposed for these ions leading to the protonated phthalic anhydride. DFT methods were used to calculate relative free energies and to determine structures of intermediate ions for these pathways. The first step of the fragmentation of [M + C2H5]+ and [M + C3H5]+ is the elimination of [RH] from an ester group. The second ester group undergoes either a McLafferty rearrangement route or a neutral loss elimination of ROH. DFT calculations (B3LYP, B3PW91 and BPW91) using 6‐311G(d,p) basis sets showed that McLafferty rearrangement of dibutyl, di(‐n‐octyl) and di(2‐ethyl‐n‐hexyl) phthalates is an energetically more favorable pathway than loss of an alcohol moiety. Prominent ions in these pathways were confirmed with deuterium labeled phthalates. Copyright © 2010 John Wiley & Sons, Ltd.
Predictors of poor sleep quality among head and neck cancer patients
Authors: Shuman Andrew G. , Duffy Sonia A. , Ronis David L. , Garetz Susan L. , McLean Scott A. , Fowler Karen E. , Terrell Jeffrey E.
Published: May 2010

Objectives/Hypothesis:

The objective of this study was to determine the predictors of sleep quality among head and neck cancer patients 1 year after diagnosis.

Study Design:

This was a prospective, multisite cohort study of head and neck cancer patients (N = 457).

Methods:

Patients were surveyed at baseline and 1 year after diagnosis. Chart audits were also conducted. The dependent variable was a self‐assessed sleep score 1 year after diagnosis. The independent variables were a 1 year pain score, xerostomia, treatment received (radiation, chemotherapy, and/or surgery), presence of a feeding tube and/or tracheotomy, tumor site and stage, comorbidities, depression, smoking, problem drinking, age, and sex.

Results:

Both baseline (67.1) and 1‐year postdiagnosis (69.3) sleep scores were slightly lower than population means (72). Multivariate analyses showed that pain, xerostomia, depression, presence of a tracheotomy tube, comorbidities, and younger age were statistically significant predictors of poor sleep 1 year after diagnosis of head and neck cancer (P < .05). Smoking, problem drinking, and female sex were marginally significant (P < .09). Type of treatment (surgery, radiation and/or chemotherapy), primary tumor site, and cancer stage were not significantly associated with 1‐year sleep scores.

Conclusions:

Many factors adversely affecting sleep in head and neck cancer patients are potentially modifiable and appear to contribute to decreased quality of life. Strategies to reduce pain, xerostomia, depression, smoking, and problem drinking may be warranted, not only for their own inherent value, but also for improvement of sleep and the enhancement of quality of life. Laryngoscope, 2010
Analytical Ultracentrifugation of Model Nanoparticles: Comparison of Different Analysis Methods
Authors: Mittal Vikas , Völkel Antje , Cölfen Helmut
Published: May 2010

Sedimentation analysis of nanoparticle (ZrO2 and SiO2) suspensions of different particle sizes in various solvents as nanoparticle model systems was carried out using interference optics in the analytical ultracentrifuge. The particles differed in their morphology: SiO2 particles were spherical, whereas ZrO2 particles were in one case spherical and in the second case non‐spherical and spherical. Different analysis programs, based on different principles of data analysis, were used for the evaluation of the size distributions of these particles, viz. SEDFIT [ls–g*(s), c(s)], UltraScan (vHW, 2DSA‐MC), SedAnal (dcdt) and VelXLAI (GFL) method and SedAnal, in order to ascertain the benefits and limitations of these analysis methods in characterising the examined nanoparticles.

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Randomization of Amyloid‐β‐Peptide(1‐42) Conformation by Sulfonated and Sulfated Nanoparticles Reduces Aggregation and Cytotoxicity
Authors: Saraiva Ana M. , Cardoso Isabel , Saraiva Maria João , Tauer Klaus , Pereira M. Carmo , Coelho Manuel A. N. , Möhwald Helmuth , Brezesinski Gerald
Published: May 2010

The amyloid‐β peptide (Aβ) plays a central role in the mechanism of Alzheimer's disease, being the main constituent of the plaque deposits found in AD brains. Aβ amyloid formation and deposition are due to a conformational switching to a β‐enriched secondary structure. Our strategy to inhibit Aβ aggregation involves the re‐conversion of Aβ conformation by adsorption to nanoparticles. NPs were synthesized by sulfonation and sulfation of polystyrene, leading to microgels and latexes. Both polymeric nanostructures affect the conformation of Aβ inducing an unordered state. Oligomerization was delayed and cytotoxicity reduced. The proper balance between hydrophilic moieties and hydrophobic chains seems to be an essential feature of effective NPs.

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Developments in the US‐SOMO Bead Modeling Suite: New Features in the Direct Residue‐to‐Bead Method, Improved Grid Routines, and Influence of Accessible Surface Area Screening
Authors: Brookes Emre , Demeler Borries , Rocco Mattia
Published: May 2010

The US‐SOMO suite provides a flexible interface for accurately computing solution parameters from 3D structures of biomacromolecules through bead‐modeling approaches. We present an extended analysis of the influence of accessible surface area screening, overlap reduction routines, and approximations for non‐coded residues and missing atoms on the computed parameters for models built by the residue‐to‐bead direct correspondence and the cubic grid methods. Importantly, by taking the theoretical hydration into account at the atomic level, the performance of the grid‐type models becomes comparable or exceeds that of the corresponding hydrated residue‐to‐bead models.

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Fabrication of Aromatic‐Aliphatic Aminoketone Polymers with Terminal Fluorine Groups
Authors: Anders Susann , Schrepp Wolfgang , Kaßner Lysann , Pohlers Andreas , Hoyer Walter , Spange Stefan
Published: May 2010

A procedure for synthesis aromatic‐aliphatic PAK, completely functionalized withp‐fluorophenyl terminal groups, is presented. This synthesis uses the nucleophilic aromatic substitution of DFB with various secondary aliphatic diamines [CH3NH(CH2)mNHCH3] (m = 3, 6, and 8) and cesium fluoride as the base catalyst in the melt. The linearity and the complete functionalization of the PAK compounds withp‐fluorophenyl terminal groups are demonstrated with the aid of MALDI TOF mass spectrometry. PAK compounds are semi‐crystalline as shown by WAXS and DSC measurements. The degree of crystallinity ranges between 2 and 25%. Nucleophilic aromatic substitution reactions in the fluorine end groups are demonstrated by reaction of PAK (m = 6) with the strongS‐nucleophile mercaptoacetic acid.

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Determination of Gel Point of Epoxy Thermosets via Electric Resistance Measurements
Authors: Wasikiewicz Jaroslaw M. , Yeates Stephen G.
Published: May 2010

A new, nickel‐coated graphite resistance‐change‐based method for gel‐point determination for epoxy‐based thermoset resins is presented and compared with DSC and rheological methods. Gelation times determined by this new method are in very good agreement with conventional techniques; this new method is potentially simpler and less time consuming than existing ones.

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Natural Fiber Welding
Authors: Haverhals Luke M. , Reichert W. Matthew , De Long Hugh C. , Trulove Paul C.
Published: May 2010

A process we term “natural fiber welding” is demonstrated by which loose fibers are transformed to create a congealed network using an IL solvent. Several examples are discussed that include cellulosic and protein‐based materials. SEM shows the fusion of fibers upon treatment. XRD and FT‐IR spectroscopy of cellulosic materials show that significant amounts of the native polymer structure are retained after the process is completed. Data suggest that material at the fiber exterior is preferentially transformed while material in the fiber core is left in the native state. Data also demonstrate that the amount of material modified can be tailored by control of variables such as the IL solvent concentration, the process temperature, and the processing time.

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One‐Step Immobilization of Protein‐Encapsulated Core/Shell Particles onto Nanofibers
Authors: Park Chul Ho , Lee Jonghwi
Published: May 2010

A novel method is described to functionalize nanofibers to form a nanocomposite with core/shell particles in order to control protein release. The nanocomposite is produced by electrically neutralizing negatively charged poly(lactic acid) nanofibers with positively charged poly[(lactic acid)‐co‐(glycolic acid)] particles via a one‐step electrohydrodynamic jetting process. The protein‐encapsulated core/shell particles exhibited no significant initial burst release or denaturation. The protein release profile was controlled by porosity and protein/polymer interactions. The method may be promising to engineer intelligent scaffolds that can fulfill the needs of biomimetic materials.

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Synthesis of Guanidinium‐Modified Hyaluronic Acid Hydrogel
Authors: Varghese Oommen P. , Kisiel Marta , Martínez‐Sanz Elena , Ossipov Dmitri A. , Hilborn Jöns
Published: May 2010

In this report, a new guanidinylating reagent is presented, which was developed without any protection/deprotection strategy and was successfully employed for linking to hyaluronan in aqueous solution. The dually functionalised HA biopolymer bearing guanidinium and hydrazide groups was synthesised to form hydrogel in less than a minute when mixed with aldehyde‐modified HA. This hydrogel exhibited higher storage modulus with enhanced stability in PBS when compared to the non‐guanidine‐containing gel. The gel shift assay showed that this biopolymer formed a stable complex with DNA as well as efficient gene transfection to cells that express HA‐receptor CD44. The toxicity studies of this polymer with fibroblast cells revealed that the cells were almost 80% viable after 4 d of incubation at high HA concentration (2.5 × 10−3 M).

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Tandem gait performance in essential tremor: Clinical correlates and association with midline tremors
Authors: Louis Elan D. , Rios Eileen , Rao Ashwini K.
Published: May 2010

Gait difficulty has been reported in essential tremor (ET) although it has been the subject of a limited number of studies. We broadly assessed these clinical correlates, including the association of gait difficulty with a variety of midline tremors (jaw, voice, neck). Tandem gait (10 steps) was assessed in 122 ET cases. Cranial tremor score (0–3) was the number of locations (neck, jaw, voice) in which tremor was present. Number of tandem mis‐steps positively correlated with age (P < 0.001), age of tremor onset (P = 0.001), and presence of neck (P < 0.001), jaw (P = 0.001), and voice tremors (P = 0.047). Number of tandem mis‐steps increased markedly with cranial tremor score: 0 (0.8 ± 1.2), 1 (1.1 ± 1.6), 2 (2.3 ± 3.0), 3 (3.7 ± 1.6) (P < 0.001). It was not correlated with severity of arm or leg tremors. ET patients with cranial tremors (neck, jaw, voice), those with older age of onset, and those of current older age are more likely to manifest tandem gait difficulty. Tandem gait difficulty was not correlated with severity of limb tremors. Tandem gait difficulty and cranial tremors in ET may both be symptomatic of the same underlying pathophysiology, a disturbance of cerebellar regulation of the midline, which is distinct from its regulation of the limbs. © 2010 Movement Disorder Society
Probabilistic Modeling of Conformational Space for 3D Machine Learning Approaches
Authors: Jahn Andreas , Hinselmann Georg , Fechner Nikolas , Henneges Carsten , Zell Andreas
Published: May 2010

We present a new probabilistic encoding of the conformational space of a molecule that allows for the integration into common similarity calculations. The method uses distance profiles of flexible atom‐pairs and computes generative models that describe the distance distribution in the conformational space. The generative models permit the use of probabilistic kernel functions and, therefore, our approach can be used to extend existing 3D molecular kernel functions, as applied in support vector machines, to build QSAR models. The resulting kernels are valid 4D kernel functions and reduce the dependency of the model quality on suitable conformations of the molecules. We showed in several experiments the robust performance of the 4D kernel function, which was extended by our approach, in comparison to the original 3D‐based kernel function. The new method compares the conformational space of two molecules within one kernel evaluation. Hence, the number of kernel evaluations is significantly reduced in comparison to common kernel‐based conformational space averaging techniques. Additionally, the performance gain of the extended model correlates with the flexibility of the data set and enables an a priori estimation of the model improvement.
In vitro derivation of germ cells from embryonic stem cells in mammals
Authors: Zhou Guang‐Bin , Meng Qing‐Gang , Li Ning
Published: May 2010

Previous reports have shown that embryonic stem (ES) cells, derived from the inner cell mass of mouse or human blastocysts, could differentiate in vitro into female and male germ cells as well as into the cell types of all three germ layers. While in one case, the ES cell‐derived germ cells have been reported to give birth to live offspring in the mouse, these cells differ in fertilization capacity from the sperm and oocytes produced in vivo as they cannot complete meiosis under in vitro conditions. The efficiency of functional germ cell isolation from ES cells is also low. According to published reports, factors such as the proper selection of feeder cells, including ovarian granulosa cells and those which could secrete bone morphogenic protein‐4 (BMP4), and the addition of retinoic acid into culture medium, could to some extent establish and improve the microenvironment ES cells rely on for differentiation into germ cells. This review briefly describes the progress of deriving germ cells from ES cells and discusses possible factors that could improve in vitro gamete production. Mol. Reprod. Dev. 77: 586–594, 2010. © 2010 Wiley‐Liss, Inc.
Epidermal growth factor (EGF) induces motility and upregulates MMP‐9 and TIMP‐1 in bovine trophoblast cells
Authors: Dilly M. , Hambruch N. , Haeger J.‐D. , Pfarrer C.
Published: May 2010

Differentiation and restricted invasion/migration of trophoblast cells are crucial for feto‐maternal communication in the synepitheliochorial placenta of cattle. EGF is expressed in the bovine placenta and likely regulates these cell properties. As cell migration and motility rely on the degradation of extracellular matrix we hypothesize that EGF is involved in the regulation of the MMP‐9/TIMP‐1 balance and thus could influence trophoblast migration, tissue remodeling, and the release of the fetal membranes after parturition. The aim of this in vitro study was to examine EGF‐mediated effects on cell motility, proliferation, and MMP‐9 and TIMP‐1 expression in cultured bovine trophoblast cells. We used a trophoblast cell line (F3) derived from bovine placentomes to examine the influence of EGF on MMP‐9 and TIMP‐1 expression by semiquantitative RT‐PCR and MMP activity by zymography. Migration assays were performed using a Boyden chamber and cell motility was measured by time‐lapse analyses. To identify the involved signaling cascades, phosphorylation of mitogen‐activated protein kinase (MAPK) 42/44 and Akt was detected by Western blot. EGF treatment increased both the abundance of MMP‐9 and TIMP‐1 mRNAs and the proteolytic activity of MMP‐9. Furthermore, EGF stimulated proliferation and migration of F3 cells. Addition of specific inhibitors of MAPK (PD98059) and/or PI3K (LY294002) activation abolished or reduced EGF‐induced effects in all experiments. In conclusion, EGF‐mediated effects stimulate migration and proliferation of bovine trophoblast cells and may be involved in bovine placental tissue remodeling and postpartum release of fetal membranes. Mol. Reprod. Dev. 77: 622–629, 2010. © 2010 Wiley‐Liss, Inc.
Real‐time adaptive sequential design for optimal acquisition of arterial spin labeling MRI data
Authors: Xie Jingyi , Clare Stuart , Gallichan Daniel , Gunn Roger N. , Jezzard Peter
Published: May 2010

An optimal sampling schedule strategy based on the Fisher information matrix and the D‐optimality criterion has previously been proposed as a formal framework for optimizing inversion time scheduling for multi‐inversion‐time arterial spin labeling experiments. Optimal sampling schedule possesses the primary advantage of improving parameter estimation precision but requires a priori estimation of plausible parameter distributions that may not be available in all situations. An adaptive sequential design approach addresses this issue by incorporating the optimal sampling schedule strategy into an adaptive process that iteratively updates the parameter estimates and adjusts the optimal sampling schedule accordingly as data are acquired. In this study, the adaptive sequential design method was experimentally implemented with a real‐time feedback scheme on a clinical MRI scanner and was tested in six normal volunteers. Adapted schedules were found to accommodate the intrinsically prolonged arterial transit times in the occipital lobe of the brain. Simulation of applying the adaptive sequential design approach on subjects with pathologically reduced perfusion was also implemented. Simulation results show that the adaptive sequential design approach is capable of incorporating pathologic parameter information into an optimal arterial spin labeling scheduling design within a clinically useful experimental time. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
In vivo MR evaluation of the effect of the CCR2 antagonist on macrophage migration
Authors: Lee Yedaun , Ryu Je‐Won , Chang Hyeujin , Sohn Jin Young , Lee Kyung Won , Woo Chul Woong , Kang Hee Jung , Jeong Seong‐Yun , Choi Eun Kyung , Lee Jin Seong
Published: May 2010

The CCR2 antagonist is a receptor antagonist for monocyte chemoattractant protein‐1 and is known to be a potential anti‐inflammatory therapeutic agent. Recently used optimized labeling techniques for superparamagnetic iron oxide, macrophage homing, and recruitment toward the infection site can be observed on in vivo MRI. This study details the effect of the CCR2 antagonist on the macrophage migration and the feasibility of in vivo MRI for assessing the inhibition of chemotactic activity by the CCR2 antagonist. On binding assay, the CCR2 antagonist inhibits the binding affinity of monocyte chemoattractant protein‐1 to CCR2. Increased expression of messenger ribonucleic acid (mRNA) and expression of CCR2 and CD11b on the cellular surface, as induced by monocyte chemoattractant protein‐1, was shown, and the effect of monocyte chemoattractant protein‐1 on CCR2 and CD11b was restricted by the CCR2 antagonist. In a migration test using the transwell system, macrophages treated with the CCR2 antagonist showed significantly decreased chemotactic migration compared to that of wild‐type macrophages. MR images of infected left calf muscles in 12 mice were obtained 24 h after administration of macrophages labeled with superparamagnetic iron oxide. MRI successfully demonstrated the effect of the CCR2 antagonist on the directional migration of macrophages. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
A high‐throughput eight‐channel probe head for murine MRI at 9.4 T
Authors: Lanz Titus , Müller Matthias , Barnes Hannah , Neubauer Stefan , Schneider Jürgen E.
Published: May 2010

Murine MRI studies are conducted on dedicated MR systems, typically equipped with ultra‐high‐field magnets (≥4.7 T; bore size: ∼12–25 cm), using a single transmit‐receive coil (volume or surface coil in linear or quadrature mode) or a transmit‐receive coil combination. Here, we report on the design and characterization of an eight‐channel volume receive‐coil array for murine MRI at 400 MHz. The array was combined with a volume‐transmit coil and integrated into one probe head. Therefore, the animal handling is fully decoupled from the radiofrequency setup. Furthermore, fixed tune and match of the coils and a reduced number of connectors minimized the setup time. Optimized preamplifier design was essential for minimizing the noise coupling between the elements. A comprehensive characterization of transmit volume resonator and receive coil array is provided. The performance of the coil array is compared to a quadrature‐driven birdcage coil with identical sensitive volume. It is shown that the miniature size of the elements resulted in coil noise domination and therefore reduced signal‐to‐noise‐ratio performance in the center compared to the quadrature birdcage. However, it allowed for 3‐fold accelerated imaging of mice in vivo, reducing scan time requirements and thus increasing the number of mice that can be scanned per unit of time. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Reduction of fast spin echo cusp artifact using a slice‐tilting gradient
Authors: Rangwala Novena , Zhou Xiaohong Joe
Published: May 2010

A “featherlike” artifact, termed a cusp artifact, is sometimes seen along the phase‐encoding direction in sagittal or coronal fast spin echo images. This artifact arises from the spins, at a location distant from the magnet isocenter, that are excited and aliased to the field of view because their precession frequency is similar to those at the isocenter. Such a situation is created due to a combination of excessive gradient nonlinearity and rapid change of the main magnetic field near the edge of the magnet where the artifact‐producing spins are located. A novel technique is proposed to reduce this artifact, in which a fast spin echo pulse sequence is modified to slightly tilt the slice selected by the radiofrequency excitation pulse away from the slice selected by the radiofrequency refocusing pulses. At the edge of the field of view, the incomplete overlap between the slices selected by the excitation and refocusing pulses effectively reduces the signals from the artifact‐prone region. In contrast, the slices overlap substantially within the field of view so that the signals are largely retained. This slice‐tilting technique has been implemented on two commercial MRI scanners operating at 3.0 T and 1.5 T, respectively, and evaluated on phantoms and human spine and extremities using clinical protocols. Both phantom and human results showed that the technique decreased the strength of the cusp artifact by at least 65% and substantially limited the spatial extent of the artifact. This technique, which can be further enhanced by a simple postprocessing step, offers significant advantages over a number of other techniques for reducing the fast spin echo cusp artifact. It can be implemented on virtually any scanner without hardware modification, complicated calibration, sophisticated image reconstruction, or patient‐handling alteration. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Computational continua
Authors: Fish Jacob , Kuznetsov Sergey
Published: May 2010

We develop a new coarse‐scale continuum formulation hereafter referred to as computational continua. By this approach, the coarse‐scale governing equations are stated on a so‐called computational continua domain consisting of disjoint union of computational unit cells, positions of which are determined to reproduce the weak form of the governing equations on the fine scale. The label ‘computational’ is conceived from both theoretical and computational considerations. From a theoretical point of view, the computational continua is endowed with fine‐scale details; it introduces no scale separation; and makes no assumption about infinitesimality of the fine‐scale structure. From computational point of view, the computational continua does not require higher‐order continuity; introduces no new degrees‐of‐freedom; and is free of higher‐order boundary conditions. The proposed continuum description features two building blocks: the nonlocal quadrature scheme and the coarse‐scale stress function. The nonlocal quadrature scheme, which replaces the classical Gauss (local) quadrature, allows for nonlocal interactions to extend over finite neighborhoods and thus introduces nonlocality into the two‐scale integrals employed in various homogenization theories. The coarse‐scale stress function, which replaces the classical notion of coarse‐scale stress being the average of fine‐scale stresses, is constructed to express the governing equations in terms of coarse‐scale fields only. Perhaps the most interesting finding of the present manuscript is that the coarse‐scale continuum description that is consistent with an underlying fine‐scale description depends on both the coarse‐scale discretization and fine‐scale details. As a prelude to introducing the computational continua framework, we unveil the relation between the generalized continua and higher‐order mathematical homogenization theory and point out to their limitations. This serves as motivation to the main part of the manuscript, which is the computational continua formulation. Copyright © 2010 John Wiley & Sons, Ltd.
Inelastic analysis of granular interfaces via computational contact homogenization
Authors: Temizer İ. , Wriggers P.
Published: May 2010

The macroscale response of granular contact interfaces is investigated. In order to circumvent the difficulties associated with a direct resolution of such heterogeneous contact problems, where highly mobile particles residing between a deformable body and a rigid surface govern the microscale dynamics, a space–time contact homogenization methodology is developed. The overall approach is based on a separation of spatial as well as temporal scales and proposes an idealized purely frictional macroscale response. The induced macroscale dissipation is directly associated with the microscale dissipation mechanisms due to (i) an inelastic constitutive response for the boundary layer of the deformable body and (ii) frictional interaction among the components of the three‐body contact system. The consequences of a viscoelastic boundary layer that sustains damage due to highly localized deformation in the vicinity of the particles are investigated extensively within a fully nonlinear computational setting that accounts for incompressibility. The effective coefficient of friction that is induced by the homogenization methodology as the fundamental macroscale observable is found to be of a non‐Amontons as well as a non‐Coulomb type. The proposed analysis framework is amenable to a multiscale implementation within a coupled micro–macro approach and yields insight into the macroscopic dynamics of similar heterogeneous interfaces with varying degrees of mobility associated with the roughness features. Copyright © 2010 John Wiley & Sons, Ltd.
Topological derivative for multi‐scale linear elasticity models applied to the synthesis of microstructures
Authors: Amstutz S. , Giusti S. M. , Novotny A. A. , de Souza Neto E. A.
Published: May 2010

This paper proposes an algorithm for the synthesis/optimization of microstructures based on anexactformula for the topological derivative of the macroscopic elasticity tensor and a level set domain representation. The macroscopic elasticity tensor is estimated by a standard multi‐scale constitutive theory where the strain and stress tensors are volume averages of their microscopic counterparts over a representative volume element. The algorithm is of simple computational implementation. In particular, it does not require artificial algorithmic parameters or strategies. This is in sharp contrast with existing microstructural optimization procedures and follows as a natural consequence of the use of the topological derivative concept. This concept provides the correct mathematical framework to treat topology changes such as those characterizing microstuctural optimization problems. The effectiveness of the proposed methodology is illustrated in a set of finite element‐based numerical examples.Copyright © 2010 John Wiley & Sons, Ltd.
Multigrid solver with automatic mesh refinement for transient elastoplastic dynamic problems
Authors: Biotteau E. , Gravouil A. , Lubrecht A. A. , Combescure A.
Published: May 2010

This paper presents an adaptive refinement strategy based on a hierarchical element subdivision dedicated to modelling elastoplastic materials in transient dynamics. At each time step, the refinement is automatic and starts with the calculation of the solution on a coarse mesh. Then, an error indicator is used to control the accuracy of the solution and a finer localized mesh is created where the user‐prescribed accuracy is not reached. A new calculation is performed on this new mesh using the non‐linear ‘Full Approximation Scheme’ multigrid strategy. Applying the error indicator and the refinement strategy recursively, the optimal mesh is obtained. This mesh verifies the error indicator on the whole structure. The multigrid strategy is used for two purposes. First, it optimizes the computational cost of the solution on the finest localized mesh. Second, it ensures information transfer among the different hierarchical meshes. A standard time integration scheme is used and the mesh is reassessed at each time step. Copyright © 2010 John Wiley & Sons, Ltd.
The statistical second‐order two‐scale method for mechanical properties of statistically inhomogeneous materials
Authors: Han Fei , Cui Junzhi , Yu Yan
Published: May 2010

A class of random composite materials with statistically inhomogeneous microstructure, for example, functionally graded materials is considered in this paper. The microstructures inside a component are gradually varying in the statistical sense. In view of this particularity, a novel statistical second‐order two‐scale (SSOTS) method is presented to predict the mechanical properties, including stiffness, and elastic limit. To develop this method, the microstructures of statistically homogeneous, and inhomogeneous materials are represented. In addition the SSOTS formulas are derived based on normalized cell depending on the position variables by a constructing way, and the algorithm procedure is described. The mechanical properties of the different inhomogeneous materials are evaluated. The numerical results are compared with the experimental findings. It shows that the SSTOS method is effective. Copyright © 2010 John Wiley & Sons, Ltd.
A new approach to plate theory based on through‐thickness homogenization
Authors: Guiamatsia I.
Published: May 2010

A new approach to linear plate theory for layered structures is introduced. The new theory distances itself from the classical strategy where through the thickness displacement functions are assumed a priori. Instead, the homogenization is based on a single assumption that the plate response is a superposition of fundamental states. An equivalent single‐layer (ESL) formulation is presented, which, for the first time, allows accurate three‐dimensional stress and strain fields to be recovered through a postprocessing strategy that is consistent with the theory's assumptions. Copyright © 2010 John Wiley & Sons, Ltd.
Inverse finite element method for large‐displacement beams
Authors: Albanesi Alejandro E. , Fachinotti Víctor D. , Cardona Alberto
Published: May 2010

A finite element model for the inverse analysis of large‐displacement beams in the elastic range is presented. The model permits determining the initial shape of a beam such that it attains the given design shape under the effect of service loads. This formulation has immediate applications in various fields such as compliant mechanism design where flexible links can be modeled as large‐displacement beams. Numerical tests for validation purposes are given, together with two design applications of flexible mechanisms with distributed compliance: a flexible gripper and a flexible S‐type clutch. Copyright © 2010 John Wiley & Sons, Ltd.
Matrix‐Padé via Lanczos solutions for vibrations of fluid–structure interaction
Authors: Liew Haw‐Ling , Pinsky Peter M.
Published: May 2010

For multiple‐frequency full‐field solutions of the boundary value problem describing small fluid–structure interaction vibration superimposed on a nominal state with prestress, we propose an efficient reduced order method by constructing the full‐field matrix‐Padé approximant of its finite element matrix function. Exploiting the matrix‐Padé via Lanczos connection, the Padé coefficients are computed in a stable and efficient way via an unsymmetric, banded Lanczos process. The full‐field Padé‐type approximant is the result of one‐sided projection onto Krylov subspace, we established its order of accuracy, which is not maximal. The superiority of this method in terms of various problem dimensions and parameters is established by complexity analysis via flop counts. Numerical examples obtained by using a model problem verified the accuracy of this full‐field matrix‐Padé approximant. Copyright © 2010 John Wiley & Sons, Ltd.
Photovoltaics literature survey (no. 78)
Authors: Shrestha Santosh
Published: May 2010

In order to help keep readers up‐to‐date in the field each issue of Progress in Photovoltaics will contain a list of recently published journal articles most relevant to its aims and scope. This list is drawn from an extremely wide range of journals, including IEEE Transactions on Electron Devices, Journal of Applied Physics, Applied Physics Letters, Progress in Photovoltaics and Solar Energy Materials and Solar Cells. To assist the reader, the list is separated into broad categories, but please note that these classifications are by no means strict. Also note that inclusion in the list is not an endorsement of a paper's quality. If you have any suggestions please email Santosh Shrestha at mailto:s.shrestha@unsw.edu.au.

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Proteome profiling reveals gender differences in the composition of human serum
Authors: Miike Koichiro , Aoki Masashi , Yamashita Ryo , Takegawa Yumiko , Saya Hideyuki , Miike Teruhisa , Yamamura Ken‐ichi
Published: May 2010

Proteome analysis using human serum is a technological advancement that will enable the discovery of novel biomarkers and biomarker patterns of various human diseases. Although proteome analysis using serum has potential in disease prevention, early diagnosis and treatment of diseases, and evaluation of pharmacotherapies, this technology is still in its infancy. Thus, we sought to develop an advanced method of conducting proteome analysis on human serum. In this study, we report the development of the semi‐comprehensive protein analytical technique, which involves the systematic use of iTRAQ labeling, HPLC, nano‐LC and MS. We compared the composition of the serum proteome in males and females using this technique and detected gender‐based differences in serum protein composition. This technology will enable the generation of databases that may ultimately lead to the discovery of specific biomarkers or biomarker patterns of various diseases.