bluuebunny/crossref_metadata_2025 huggingface dataset:
Methyl palmitate inhibits lipopolysaccharide‐stimulated phagocytic activity of rat peritoneal macrophages
Authors: Sarkar Swapna , Khan M. Firoze , Kaphalia Bhupendra S. , Ansari G. A. S.
Published: December 2006

Macrophages, in general, are critical effectors of body's immune system. Chemical inhibition of phagocytic activity of such macrophages as Kupffer cells has been extensively studied. We have earlier shown that methyl palmitate (MP) inhibits the activation of Kupffer cells. To evaluate the potential of MP to inhibit the activation of other macrophages, we treated rat peritoneal macrophages with varying concentrations of MP. Its treatment led to a dose‐dependent inhibition of phagocytic activity, which was found to be 34%, 47%, and 66% at 0.25, 0.50, and 1.0 mM MP, respectively, as measured by latex bead uptake. When MP‐treated peritoneal macrophages were stimulated with lipopolysaccharide (LPS), the nitric oxide (.NO) release was inhibited at 6 h, while cyclooxygenase‐2 expression decreased after 24 h. The treatment with MP increased the release of interleukin (IL)‐10 in the LPS‐treated cells at 6 h, while IL‐6 and tumor necrosis factor‐α were significantly increased both at 6 and 24 h. Our data suggest that MP inhibits phagocytic activity and .NO production similar to that observed in isolated Kupffer cells. Therefore, inhibition of phagocytosis by MP may be a general phenomenon, and it could be used as an inhibitor of macrophage function. © 2006 Wiley Periodicals, Inc. J Biochem Mol Toxicol 20:302–308, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20150
Systemic treatments with the low‐calcemic 1,25(OH)2D3 analogs JKF or QW increase both the morphological and biochemical responses to estradiol‐17β in rat tibiae
Authors: Somjen D. , Katzburg S. , Posner G.H. , Livne E. , Kaye A.M.
Published: December 2006

We demonstrated previously that daily injection for 3 days of the less calcemic vitamin D analogs: JK 1624 F2‐2 (JKF) and QW 1624F2‐2 (QW) followed by estradiol‐17β (E2) in female rats upregulated creatine kinase‐specific activity (CK) in skeletal tissues. In this study, we evaluated both histomorphological and biochemical changes due to a regime of 4 days treatment with JKF or QW, followed by injection of E2 on day 5, repeated for 2.5 months. Ovariectomized female rats (Ovx) were injected 2 weeks after surgery, with JKF or QW at 0.2 ng/g BW followed by injections of E2 (1 µg/rat) on day 5 of each week for 2.5 months. Rats were sacrificed 24 h after the last injection and bones were analyzed. JKF alone decreased growth plate width, increased % total bone volume (%TBV), with no change in cortical thickness. In contrast, QW restored growth plate width and %TBV with no change in cortical thickness. Combined with E2, JKF restored %TBV and growth plate width but with no change in cortical thickness, while QW restored significantly all parameters including cortical thickness. Moreover, there was also an increase in the responsiveness of CK to E2 in epiphyseal cartilage and diaphyseal bone but not in uterus. Thus, vitamin D less calcemic analogs increased responsiveness to E2 morphologically as well as biochemically. We, therefore, conclude that combined treatment of less calcemic analogs vitamin D and E2 might be superior for treatment of bone damage caused by ovariectomy in female rats and might be applied for post‐menopausal osteoporosis. J. Cell. Biochem. 100: 1406–1414, 2007. © 2006 Wiley‐Liss, Inc.
Smooth muscle α‐actin expression and myofibroblast differentiation by TGFβ are dependent upon MK2
Authors: Sousa Anne Marie , Liu Tiegang , Guevara Oscar , Stevens JoAnne , Fanburg Barry L. , Gaestel Matthias , Toksoz Deniz , Kayyali Usamah S.
Published: December 2006

Fibroblasts play a major role in processes such as wound repair, scarring, and fibrosis. Differentiation into myofibroblasts, characterized by upregulation of smooth muscle α‐actin (smα) in response to profibrotic agents such as TGFβ is believed to be an important step in fibrosis. Therefore, elucidating mechanisms of myofibroblast differentiation might reveal novel targets in treating diseases such as idiopathic pulmonary fibrosis (IPF). MK2 is a kinase substrate of p38 MAP kinase that mediates some effects of p38 activation on the actin cytoskeleton. Using mouse embryonic fibroblasts (MEF) from MK2 knockout (MK2−/−) mice, we demonstrate that disrupting expression of MK2 expression reduces filamentous actin and stress fibers. It also causes MK2−/− MEF to express less smα than their corresponding wild‐type (WT) MEF at baseline and in response to TGFβ. Furthermore, TGFβ causes downregulation of smα in MK2−/− MEF, instead of upregulation observed in WT MEF. Expression of other fibroblast markers, such as collagen, is not altered in MK2−/− MEF. Our results further suggest that downregulation of smα in MK2−/− MEF is not due to lack of activation of serum responsive promoter elements, but probably due to reduced smα message stability in these cells. These results indicate that MK2 plays a key role in regulation of smα expression, and that targeting MK2 might present a therapeutic approach in managing conditions such as pulmonary fibrosis. J. Cell. Biochem. 100: 1581–1592, 2007. © 2006 Wiley‐Liss, Inc.
Swimming and cleaning in the free‐swimming phase of Argulus larvae (crustacea, branchiura)—Appendage adaptation and functional morphology
Authors: Møller Ole Sten , Olesen Jørgen , Waloszek Dieter
Published: December 2006

The free‐swimming early larval stages of Argulus foliaceus (Linneaus) (Branchiura) are studied using digital video, light microscopy, and SEM. We analyze and document the mode of swimming in the hatching stage of A. foliaceus and the subsequent juvenile stages with fully developed thoracopods. We present new observations and an analysis of the functional morphology of a cleaning behavior in the first stage. This stage swims very efficiently using the large exopods of the second antennae in concert with the mandibular palp (naupliar limbs), while the subsequent stages use the now developed thoracopods for propulsion. This posterior shift in propulsion is similar to—but independent from—what is seen in other crustaceans. The hatching stage has previously been referred as a “metanauplius” but as the first and second maxillae are developed and active, and buds of all four thoracopods are present, it is too advanced to be included in the naupliar phase. The hooks of the first antennae and the distal hooks of the maxillae are demonstrated to function not only as attachment organs (to the host), but also to play a significant role in the cleaning of the naupliar swimming appendages. A digital video‐based analysis of the swimming mode is provided. The larval swimming pattern is generally similar to that of other crustaceans such as Branchiopoda and Cirripedia, but autapomorphies of the Branchiura include the following: 1) While actively swimming, the naupliar appendages are almost straight during the recovery stroke and 2) they have a relatively small deflection during movement (∼25° or ∼35° for mandible and second antenna respectively), 3) the larval mandible has a uniramous palp which is the retained exopod. The morphological implications of the transition from the possibly nonfeeding pelagic, or free‐swimming, first larval stage to the feeding, parasitic second stage are discussed and compared with other crustaceans. J. Morphol., 2007. © 2006 Wiley‐Liss, Inc.
Clonazepam quantification in human plasma by high‐performance liquid chromatography coupled with electrospray tandem mass spectrometry in a bioequivalence study
Authors: Cavedal Luiz E. , Mendes Fabiana D. , Domingues Claudia C. , Patni Anil K. , Monif Tausif , Reyar Simrit , Pereira Alberto dos S. , Mendes Gustavo D. , De Nucci Gilberto
Published: December 2006

A rapid, sensitive and specific method for quantifying clonazepam in human plasma using diazepam as the internal standard (IS) is described. The analyte and the IS were extracted from plasma by liquid‐liquid extraction using a hexane/diethylether (20 : 80, v/v) solution. The extracts were analysed by high‐performance liquid chromatography coupled with electrospray tandem mass spectrometry (HPLC‐MS‐MS). Chromatography was performed on a Jones Genesis C8 4 µm analytical column (100 × 2.1 mm i.d.). The method had a chromatographic run time of 3.0 min and a linear calibration curve over the range 0.5–50 ng/ml (r2 > 0.9965). The limit of quantification was 0.5 ng/ml. This HPLC/MS/MS procedure was used to assess the bioequivalence of two clonazepam 2 mg tablet formulations (clonazepam test formulation from Ranbaxy Laboratories Ltd and Rivotril from Roche Laboratórios Ltda as standard reference formulation). Copyright © 2006 John Wiley & Sons, Ltd.
Ion trap mass spectrometry on a comet nucleus: the Ptolemy instrument and the Rosetta space mission
Authors: Todd John F. J. , Barber Simeon J. , Wright Ian P. , Morgan Geraint H. , Morse Andrew D. , Sheridan Simon , Leese Mark R. , Maynard Jon , Evans Suzanne T. , Pillinger Colin T. , Drummond Duncan L. , Heys Samantha C. , Huq S. Ejaz , Kent Barry J. , Sawyer Eric C. , Whalley Martin S. , Waltham Nicholas R.
Published: December 2006

In May 2014, the Rosetta spacecraft is scheduled to rendezvous with the comet Churyumov–Gerasimenko (‘67P’). One of the instruments on board the ‘Lander’ which will descend on to the surface of the comet is a miniaturised GC/MS system that incorporates an ion trap mass spectrometer, specially developed for isotope ratio analysis. This article describes the development and optimisation of the ion trap for this unique application, and presents a summary of the range of pre‐programmed experiments that will contribute to the characterisation of the solid and volatile cometary materials. Copyright © 2006 John Wiley & Sons, Ltd.
Rapid on‐plate and one‐pot derivatization of carbonyl compounds for enhanced detection by reactive matrix LDI‐TOF MS using the tailor‐made reactive matrix, 4‐dimethylamino‐6‐(4‐methoxy‐1‐naphthyl)‐1,3,5‐triazine‐2‐hydrazine (DMNTH)
Authors: Mugo Samuel M. , Bottaro Christina S.
Published: December 2006

In this study, a very sensitive and economical high‐throughput methodology has been developed for the analysis of small carbonyl compounds using rapid derivatization with 4‐dimethylamino‐6‐(4‐methoxy‐1‐naphthyl)‐1,3,5‐triazine‐2‐hydrazine (DMNTH), a derivatizing agent developed by the Karst group at the University of Münster. DMNTH is highly ionizable by the UV laser and reacts selectively and rapidly with carbonyl moieties. The resulting hydrazone is easily detectable by laser desorption ionization time of flight mass spectrometry (LDI‐TOF MS), eliminating the need for the matrix assisted variant (MALDI) and the associated issue of matrix optimization, which greatly simplifies the analysis. It has been demonstrated that a range of carbonyl compounds can be conveniently analyzed by this reactive matrix LDI‐TOF MS (RM‐LDI‐TOF MS) procedure and that furfural DMNThydrazone (prior labeled and labeled in situ) can be used as an internal standard for semiquantitative analysis. Amounts as low as 0.5 ng ml−1 of 4‐methoxybenzaldehyde have been detected using a one‐pot derivatization methodology. Rapid on‐plate derivatization was also found to be a simple approach for fast and reliable screening of various analytes, although with slightly higher detection limits. To test its applicability in complex matrices, analysis of furfural spiked in beer has been demonstrated. This RM‐LDI‐TOF MS method shows considerable promise for the analysis of carbonyl compounds in water, particularly for disinfection by‐products that result from reaction of natural organic matter with oxidative disinfectants. Copyright © 2006 John Wiley & Sons, Ltd.
Hypoglycemia reduces the blood‐oxygenation level dependent signal in primary auditory and visual cortex: A functional magnetic resonance imaging study
Authors: Driesen Naomi R. , Goldberg Philip A. , Anderson Adam W. , Tang Lin , Flanagan Daniel E. , Sherwin Robert S. , Gore John C.
Published: December 2006

Studies of the effects of hypoglycemia on the brain using neurocognitive testing have suggested that mainly complex functions subserved by secondary and tertiary cortex are affected by mild to moderate hypoglycemia and that intensively treated patients with Type I diabetes mellitus (T1DM) may have altered sensitivity to the central nervous system effects of hypoglycemia. Functional magnetic resonance imaging provides a sensitive, regionally‐specific probe of possible neurophysiologic changes related to hypoglycemia in the brain. Eleven intensively‐treated T1DM patients and 11 matched non‐diabetic controls took part in a 2‐day protocol in which functional magnetic resonance imaging (MRI) was used to measure changes in the patterns of brain activation produced by simple auditory and visual stimuli in different conditions. On one day, participants were euglycemic the entire time. On the other day, an initial 50‐min euglycemic period was followed by a 50‐min hypoglycemic period. Results indicated that hypoglycemia reduced the amplitude of the blood‐oxygenation level dependent response in primary auditory and visual cortex to simple auditory and visual stimuli. The latency and duration of the transient hemodynamic response function were not affected. Responses to hypoglycemia were similar in diabetic and non‐diabetic participants. These results suggest that mild to moderate hypoglycemia may alter the balance of blood flow and oxygen extraction when glucose levels are lowered. Intensively‐treated T1DM, with its attendant frequent hypoglycemic episodes, did not seem to alter hypoglycemic responses in primary visual and auditory cortex. © 2006 Wiley‐Liss, Inc.
Thermal decomposition of methyl β‐hydroxyesters in m‐xylene solution
Authors: Zapata Edilma , Gaviria Jair , Quijano Jairo
Published: December 2006

The products and kinetics of the thermal decomposition of several methyl‐β‐hydroxyesters in m‐xylene solution have been studied. It has been shown that all β‐hydroxyesters studied pyrolyze to form a mixture of methyl acetate and the corresponding aldehyde or ketone and that the decomposition follows first‐order kinetics and appears to be homogeneous and unimolecular. The rate pyrolysis of methyl‐3‐hydroxypropanoate, methyl‐3‐hydroxybutanoate, and methyl‐3‐hydroxy‐3‐methylbutanoate has been measured between 250 and 320°C. The relative rates of primary, secondary, and tertiary alcohols at 553 K are 1.0, 8.5 and 54.1, respectively. The absence of large substituent effects indicates that little charge separation occurs during the breaking of carbon–carbon single bond. The activation entropy is compatible with a semipolar six‐membered cyclic transition state postulated for other β‐hydroxy compounds. © 2006 Wiley Periodicals, Inc. Int J Chem Kinet 39: 92–96, 2007
Synthesis and thermal decomposition reaction kinetics of complexes of [Sm2(m‐ClBA)6(phen)2] · 2H2O and [Sm2(m‐BrBA)6(phen)2] · 2H2O
Authors: Zhang Jian Jun , Ren Ning , Bai Ji Hai , Xu Su Ling
Published: December 2006

Complexes of [Sm2(m‐ClBA)6(phen)2] · 2H2O and [Sm2(m‐BrBA)6(phen)2] · 2H2O (m‐ClBA = m‐chlorobenzoate, m‐BrBA = m‐bromobenzoate, and phen = 1,10‐phenanthroline) were prepared and characterized by elemental analysis and IR spectra. The thermal decomposition processes of the two complexes were studied by means of TG–DTG and IR techniques. Their thermal decomposition kinetics were investigated from the analysis of the TG and DTG curves by jointly using a new method proposed by us and a newly nonlinear isoconversional integral method. © 2006 Wiley Periodicals, Inc. Int J Chem Kinet 39: 67–74, 2007
Thermolytic investigations on nickel(II) complexes of 4‐N‐(4′‐antipyrylmethylidene)aminoantipyrine with various counterions
Authors: Madhu N. T. , Radhakrishnan P. K. , Linert Wolfgang
Published: December 2006

Phenomenological characteristics and kinetic and mechanistic aspects of the thermal decomposition of nitrate, chloride, bromide, and iodide complexes of nickel(II) with 4‐N‐(4′‐antipyrylmethylidene)aminoantipyrine have been studied using thermogravimetric (TG) and differential thermogravimetric (DTG) techniques. Kinetic parameters such as activation energy, preexponential factor, and entropy of activation were quantified. The rate‐controlling process in all stages of decomposition was found to be based on random nucleation with one nucleus on each particle according to the Mampel model. © 2006 Wiley Periodicals, Inc. Int J Chem Kinet 39: 53–58, 2007
Kinetics and mechanism of gas‐phase pyrolysis of N‐aryl‐3‐oxobutanamide ketoanilides, their 2‐arylhydrazono derivatives, and related compounds
Authors: Malhas Rana N. , Al‐Awadi Nouria A. , El‐Dusouqui Osman M. E.
Published: December 2006

Rates and products of reaction and Arrhenius activation parameters were determined for the gas‐phase thermolysis of 14 substrates of the title compounds using sealed pyrex reactor tubes and HPLC/UV‐VIS to monitor substrate pyrolysis. The 14 compounds under study are N‐phenyl‐3‐oxo‐ (1), N‐(p‐chlorophenyl)‐3‐oxo‐ (2), N‐(p‐methylphenyl)‐3‐oxo‐ (3), and N‐(p‐methoxyphenyl)‐3‐oxobutanamide (4), in addition to (i) four substrates (5–8) obtained by the replacement of the pairs of methylene hydrogens at the 2‐position of compounds (1–4), each pair by a phenylhydrazono group; (ii) three arylhydrazono derivatives (9–11) in which Cl, CH3, or OCH3 groups are substituted at the para position of the phenylhydrazono moiety of compound 5; (iii) 3‐oxobutanamide (acetoacetamide, 12), N‐phenyl‐3‐oxo‐3‐phenylpropanamide (13), and N,N′‐diphenylpropanediamide (14). The reactions were conducted over 374–546 K temperature range, and the values of the Arrhenius log A(s−1) and Ea(kJ mol−1) of these reactions were, respectively, 12.0 ± 2.0 and 119.2 ± 17.0 for the ketoanilides (1–4, 12–14), and 13.0 ± 0.7 and 157.5 ± 8.6 for the arylhyrazono compounds (5–11). Kinetically, the arylhydrazono derivatives were found to be ca. 1.4 × 103 to 5.7 × 103 times less reactive than the parent ketoanilides. A mechanism is proposed to account for reaction products and to rationalize molecular reactivities. © 2006 Wiley Periodicals, Inc. Int J Chem Kinet 39: 82–91, 2007
Shock‐tube studies on the reactions of dimethyl ether with oxygen and hydrogen atoms
Authors: Takahashi K. , Yamamoto O. , Inomata T. , Kogoma M.
Published: December 2006

The reactions of dimethyl ether (CH3OCH3, DME) with O(3P) and H atoms have been studied at high temperatures by using a shock tube apparatus coupled with atomic resonance absorption spectroscopy (ARAS). The rate coefficients for the reactions CH3OCH3 + O(3P) → CH3OCH2 + OH (1) and CH3OCH3 + H → CH3OCH2 + H2 (2) were experimentally determined from the decay of O(3P) and H atoms as:

equation image

These results show that DME can react with O(3P) atoms more easily than with H atoms. By combining these results with the previous lower temperature data, we obtained the following modified Arrhenius expressions applied over the wide temperature range between 300 and 1500 K:

equation image

Both reactions of DME are faster than those of ethane, because the dissociation energy of the CH bond in DME is smaller. Furthermore, the rate coefficients for reactions (1) and (2) were calculated with the transition‐state theory (TST). Structural parameters and vibrational frequencies of the reactants and the transition states required for the TST calculation were obtained from the MP2(full)/6‐31G(d) ab initio molecular orbital (MO) calculation. The energy barrier, E‡0, was adjusted until the TST rate coefficient most closely matched the observed one. The fitting results of E(1) = 23 kJ mol−1 and E(2) = 34 kJ mol−1 were in agreement with the G2 energy barriers, within the expected uncertainty, demonstrating that the experimentally determined rate coefficients were theoretically valid. © 2006 Wiley Periodicals, Inc. 39: 97–108, 2007
Micro traps for quantum information processing and precision force sensing
Authors: Birkl G. , Fortágh J.
Published: December 2006

We review recent experimental progress towards quantum information processing and precision force sensing using neutral atoms in micro traps. Microscopic potential structures as generated by optical or electronic microstructures (micro traps) allow for a versatile manipulation of quantum states of atoms and of ultracold atomic quantum gases. Most recent experimental results include the implementation of single‐qubit‐operations in both, optical and magnetic micro traps, as well as in the demonstration of matter‐wave interferometer using Bose‐Einstein condensates coherently split in micro traps.
Improved staining method for determining the extent of thermal damage to cells
Authors: Sherwood Margaret E. , Flotte Thomas J.
Published: December 2006

Background and Objective

Enzyme histochemical stains of frozen sections have been used by investigators to assess thermal damage. The assessment of thermal damage to cells in lipid‐rich tissues such as subcutaneous tissue and sebaceous glands can be difficult due to the quality of frozen sections of such tissues. The purpose of this study is to develop an improved method for this type of evaluation.

Study Design/Materials and Methods

Thick frozen sections of thermally damaged pig and human skin were stained for lactate dehydrogenase. The sections were fixed in formalin and processed for paraffin‐embedded sections.

Results

The sections showed well‐defined localization of the enzymatic deposits as well as preservation of the tissue architecture.

Conclusion

The paraffin‐embedded lactate dehydrogenase stained sections provide improved evaluation of thermally damaged tissues, particularly the lipid rich tissues. Lasers Surg. Med. 39:128–131, 2007. © 2007 Wiley‐Liss, Inc.
Imaging the cavernous nerves in the rat prostate using optical coherence tomography
Authors: Fried Nathaniel M. , Rais‐Bahrami Soroush , Lagoda Gwen A. , Chuang Ying , Burnett Arthur L. , Su Li‐Ming
Published: December 2006

Introduction

Improvements in identification, imaging, and visualization of the cavernous nerves (CNs) during radical prostatectomy, which are responsible for erectile function, may improve nerve preservation and post‐operative potency. Optical coherence tomography (OCT) is capable of real‐time, high‐resolution, cross‐sectional, in vivo tissue imaging. The rat prostate serves as an excellent model for studying the use of OCT for imaging the CNs, as the rat CN is a large, visible, and distinct bundle allowing for easy identification with OCT in addition to histologic confirmation.

Materials and Methods

Imaging was performed with the Niris OCT system and a handheld 8 Fr probe, capable of acquiring real‐time images with 11‐µm axial and 25‐µm lateral resolution in tissue. Open surgical exposure of the prostate was performed on a total of six male rats, and OCT images of the prostate, CN, pelvic plexus ganglion, seminal vesicle, blood vessels, and periprostatic fat were acquired. CN electrical stimulation with simultaneous intracorporeal pressure measurements was performed to confirm proper identification of the CNs. The prostate and CNs were also processed for histologic analysis and further confirmation.

Results

Cross‐sectional and longitudinal OCT images of the CNs were acquired and compared with histologic sections. The CN and ganglion could be differentiated from the surrounding prostate gland, seminal vesicle, blood vessels, bladder, and fatty tissue.

Conclusions

We report preliminary results of OCT images of the rat CNs with histologic correlation and erectile stimulation measurements, thus providing interpretation of prostate structures as they appear in OCT images. Lasers Surg. Med. © 2006 Wiley‐Liss, Inc.
On the representation formula for well‐ordered elastic composites: a convergence of measure approach
Authors: Ou Miao‐Jung
Published: December 2006

The aim of this paper is to derive an integral representation formula for the effective elasticity tensor for a two‐component well‐ordered composite of elastic materials without using a third reference medium and without assuming the completeness of the eigenspace of the operator Ĝ defined in (2.16) in (J. Mech. Phys. Solids 1984; 32(1):41–62). As shown in (J. Mech. Phys. Solids 1984; 32(1):41–62) and (Math. Meth. Appl. Sci. 2006; 29(6):655–664), this integral representation formula implies a relation which links the effective elastic moduli to the N‐point correlation functions of the microstructure. Such relation not only facilitates a powerful scheme for systematic incorporation of microstructural information into bounds on the effective elastic moduli but also provides a theoretical foundation for de‐homogenization. The analysis presented in this paper can be generalized to an n‐component composite of elastic materials. The relations developed here can be applied to the de‐homogenization for a special class of linear viscoelastic composites. The results will be presented in another paper. Copyright © 2006 John Wiley & Sons, Ltd.
Localized failure of fibre‐reinforced elastic–plastic materials subjected to plane strain loading
Authors: Perić Dunja , Rasheed Hayder A.
Published: December 2006

We consider discontinuous bifurcations as the indicator of a localized failure for a class of composites that are characterized by elastic fibres reinforcing an elastic–plastic matrix. A macroscopic tangent stiffness tensor for the fibre‐reinforced composite is developed by consistently homogenizing the contribution of fibres in a spherical representative volume element. Analytical solutions are derived for the critical hardening modulus and corresponding bifurcation directions for the case of plane strain loading. Properties of the solutions are further illustrated on the example of the non‐associated Drucker–Prager model at onset of yielding. Results show that presence of fibres decreases the critical hardening modulus, thus inhibiting the onset of strain localization. The rate of decrease in the critical hardening modulus is the highest for pure shear, followed by uniaxial tension, uniaxial compression, biaxial tension and biaxial compression. The main fibre parameters that control the onset of strain localization are their volumetric content and their stiffness modulus whereby very stiff fibres can produce the most significant decrease in the critical hardening modulus, especially for the state of biaxial tension. The critical hardening modulus for the non‐associated Drucker–Prager model exhibits a full range of localization modes including compaction bands, dilation bands, and transition in the form of shear bands regardless of the presence of fibres. Presence of fibres affects bifurcation directions, except in the case when Poisson's ratio of the matrix is equal to 0.25. The results demonstrate stabilizing effects of fibres by which they provide the control against the onset of strain localization. Copyright © 2006 John Wiley & Sons, Ltd.
Accelerating strategies to the numerical simulation of large‐scale models for sequential excavation
Authors: Noronha M. , Duenser Ch. , Beer G.
Published: December 2006

In this paper, a novel combination of well‐established numerical procedures is explored in order to accelerate the simulation of sequential excavation. Usually, large‐scale models are used to represent these problems. Due to the high number of equations involved, the solver algorithm represents the critical aspect which makes the simulation very time consuming. The mutable nature of the excavation models makes this problem even more pronounced. To accomplish the representation of geometrical and mechanical aspects in an efficient and simple manner, the proposed solution employs the boundary element method with a multiple‐region strategy. Together with this representational system, a segmented storage scheme and a time‐ordered tracking of the changes form an adequate basis for the usage of fast updating methods instead of frontal solvers. The present development employs the Sherman–Morrison–Woodbury method to speed up the calculation due to sequential changes. The efficiency of the proposed framework is illustrated through the simulation of test examples of 2D and 3D models. Copyright © 2006 John Wiley & Sons, Ltd.
Element‐based preconditioners for elasto‐plastic problems in geotechnical engineering
Authors: Augarde C. E. , Ramage A. , Staudacher J.
Published: December 2006

Iterative solvers are widely regarded as the most efficient way to solve the very large linear systems arising from finite element models. Their memory requirements are small compared to those for direct solvers. Consequently, there is a major interest in iterative methods and particularly the preconditioning necessary to achieve rapid convergence. In this paper we present new element‐based preconditioners specifically designed for linear elasticity and elasto‐plastic problems. The study presented here is restricted to simple associated plasticity but should find wide application in other plasticity models used in geotechnics. Copyright © 2006 John Wiley & Sons, Ltd.
BXL‐628, a vitamin D receptor agonist effective in benign prostatic hyperplasia treatment, prevents RhoA activation and inhibits RhoA/Rho kinase signaling in rat and human bladder
Authors: Morelli Annamaria , Vignozzi Linda , Filippi Sandra , Vannelli Gabriella Barbara , Ambrosini Stefano , Mancina Rosa , Crescioli Clara , Donati Silvia , Fibbi Benedetta , Colli Enrico , Adorini Luciano , Maggi Mario
Published: December 2006

BACKGROUND

BXL‐628 is a calcitriol analog shown to decrease prostate growth in preclinical and clinical studies. BPH symptoms are generated not only by prostate overgrowth but also by bladder overactivity, resulting from an increased RhoA/Rho‐kinase signaling. Because bladder smooth muscle cells express VDR, we studied effects of BXL‐628 on this pathway.

METHODS

RhoA and Rho‐kinase gene expression and functional activity were studied in rat and human bladder smooth muscle by real‐time RT‐PCR, immuno‐kinase assays, western blot analysis, confocal microscopy, in vitro contractility, and cell migration.

RESULTS

In bladder smooth muscle, carbachol responsiveness was delayed and Rho‐kinase activity reduced by BXL‐628 treatment because of impaired RhoA membrane translocation and activation. Accordingly, RhoA‐mediated biological functions, such as cell migration and cytoskeleton remodeling were also inhibited by BXL‐628.

CONCLUSIONS

BXL‐628 inhibits RhoA/Rho‐kinase signaling, a calcium sensitizing pathway, suggesting its possible clinical use in the treatment of altered bladder contractility often associated with BPH‐induced lower urinary tract symptoms. Prostate 67:234–247, 2007. © 2006 Wiley‐Liss, Inc.
Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling
Authors: Li Xin , Jacobson Matthew P. , Zhu Kai , Zhao Suwen , Friesner Richard A.
Published: December 2006

We have developed a new method (Independent Cluster Decomposition Algorithm, ICDA) for creating all‐atom models of proteins given the heavy‐atom coordinates, provided by X‐ray crystallography, and the pH. In our method the ionization states of titratable residues, the crystallographic mis‐assignment of amide orientations in Asn/Gln, and the orientations of OH/SH groups are addressed under the unified framework of polar states assignment. To address the large number of combinatorial possibilities for the polar hydrogen states of the protein, we have devised a novel algorithm to decompose the system into independent interacting clusters, based on the observation of the crucial interdependence between the short range hydrogen bonding network and polar residue states, thus significantly reducing the computational complexity of the problem and making our algorithm tractable using relatively modest computational resources. We utilize an all atom protein force field (OPLS) and a Generalized Born continuum solvation model, in contrast to the various empirical force fields adopted in most previous studies. We have compared our prediction results with a few well‐documented methods in the literature (WHATIF, REDUCE). In addition, as a preliminary attempt to couple our polar state assignment method with real structure predictions, we further validate our method using single side chain prediction, which has been demonstrated to be an effective way of validating structure prediction methods without incurring sampling problems. Comparisons of single side chain prediction results after the application of our polar state prediction method with previous results with default polar state assignments indicate a significant improvement in the single side chain predictions for polar residues. Proteins 2007. © 2006 Wiley‐Liss, Inc.
A topologically related singularity suggests a maximum preferred size for protein domains
Authors: Zbilut Joseph P. , Chua Gek Huey , Krishnan Arun , Bossa Cecilia , Rother Kristian , Webber Charles L. , Giuliani Alessandro
Published: December 2006

A variety of protein physicochemical as well as topological properties, demonstrate a scaling behavior relative to chain length. Many of the scalings can be modeled as a power law which is qualitatively similar across the examples. In this article, we suggest a rational explanation to these observations on the basis of both protein connectivity and hydrophobic constraints of residues compactness relative to surface volume. Unexpectedly, in an examination of these relationships, a singularity was shown to exist near 255–270 residues length, and may be associated with an upper limit for domain size. Evaluation of related G‐factor data points to a wide range of conformational plasticity near this point. In addition to its theoretical importance, we show by an application of CASP experimental and predicted structures, that the scaling is a practical filter for protein structure prediction. Proteins 2007. © 2006 Wiley‐Liss, Inc.
Strategies for high‐throughput comparative modeling: Applications to leverage analysis in structural genomics and protein family organization
Authors: Mirkovic Nebojsa , Li Zhaohui , Parnassa Andrew , Murray Diana
Published: December 2006

The technological breakthroughs in structural genomics were designed to facilitate the solution of a sufficient number of structures, so that as many protein sequences as possible can be structurally characterized with the aid of comparative modeling. The leverage of a solved structure is the number and quality of the models that can be produced using the structure as a template for modeling and may be viewed as the “currency” with which the success of a structural genomics endeavor can be measured. Moreover, the models obtained in this way should be valuable to all biologists. To this end, at the Northeast Structural Genomics Consortium (NESG), a modular computational pipeline for automated high‐throughput leverage analysis was devised and used to assess the leverage of the 186 unique NESG structures solved during the first phase of the Protein Structure Initiative (January 2000 to July 2005). Here, the results of this analysis are presented. The number of sequences in the nonredundant protein sequence database covered by quality models produced by the pipeline is ∼39,000, so that the average leverage is ∼210 models per structure. Interestingly, only 7900 of these models fulfill the stringent modeling criterion of being at least 30% sequence‐identical to the corresponding NESG structures. This study shows how high‐throughput modeling increases the efficiency of structure determination efforts by providing enhanced coverage of protein structure space. In addition, the approach is useful in refining the boundaries of structural domains within larger protein sequences, subclassifying sequence diverse protein families, and defining structure‐based strategies specific to a particular family. Proteins 2007. © 2006 Wiley‐Liss, Inc.
The role of phosphorylation on the structure and dynamics of phospholamban: A model from molecular simulations
Authors: Pantano Sergio , Carafoli Ernesto
Published: December 2006

Phospholamban (PLB) is a small membrane protein that regulates the activity of the calcium ATP‐ase in the cardiac, slow‐twitch, and smooth muscle sarcoplasmic reticulum through the reversible phosphorylation of Ser16. We present here a comparative molecular dynamics study of unmodified and phosphorylated PLB immersed in a phospholipid membrane. The study has been performed under different ionic strength conditions, using the NMR structures of two PLB variants determined in mixed organic solvent and dodecylphosphocholine micelles. The simulations indicate that all PLB forms studied display a highly dynamic behavior of the N‐terminal cytoplasmic moiety, with a decrease of its helical content in the phosphorylated forms. The cytoplasmic domain undergoes large collective motions sampling conformations parallel as well as perpendicular to the membrane surface in all the simulations. The transmembrane domain retains a tightly folded helical conformation with a small tilt with respect to the membrane plane probably induced by the presence of Asn30 and Asn34 within the hydrophobic environment. Furthermore, the phosphoric group on Ser16 establishes transient electrostatic interactions with the phospholipid heads. We propose a model in which phosphorylation diminishes the probability of interactions of PLB with residues near Lys400 in the SERCA pump, thus relieving itsinhibition. Proteins 2007 © 2006 Wiley‐Liss, Inc.
Ancestral sequence evolutionary trace and crystal structure analyses of alkaline α‐amylase from Bacillus sp. KSM‐1378 to clarify the alkaline adaptation process of proteins
Authors: Shirai Tsuyoshi , Igarashi Kazuaki , Ozawa Tadahiro , Hagihara Hiroshi , Kobayashi Tohru , Ozaki Katsuya , Ito Susumu
Published: December 2006

The crystal structure of alkaline liquefying α‐amylase (AmyK) from the alkaliphilic Bacillus sp. KSM‐1378 was determined at 2.1 Å resolution. The AmyK structure belongs to the GH13 glycoside hydrolase family, which consists of three domains, and bound three calcium and one sodium ions. The alkaline adaptation mechanism of AmyK was investigated by the ancestral sequence evolutionary trace method and by extensive comparisons between alkaline and nonalkaline enzyme structures, including three other protein families: protease, cellulase, and phosphoserine aminotransferase. The consensus change for the alkaline adaptation process was a decrease in the Lys content. The loss of a Lys residue is associated with ion pair remodeling, which mainly consists of the loss of Lys–Asp/Glu ion pairs and the acquisition of Arg ion pairs, preferably Arg–Glu. The predicted replacements of the positively charged amino acids were often, although not always, used for ion pair remodeling. Proteins 2007. © 2006 Wiley‐Liss, Inc.
Role of intrinsic disorder in transient interactions of hub proteins
Authors: Singh Gajinder Pal , Ganapathi Mythily , Dash Debasis
Published: December 2006

Hubs in the protein–protein interaction network have been classified as “party” hubs, which are highly correlated in their mRNA expression with their partners while “date” hubs show lesser correlation. In this study, we explored the role of intrinsic disorder in date and party hub interactions. The data reveals that intrinsic disorder is significantly enriched in date hub proteins when compared with party hub proteins. Intrinsic disorder has been largely implicated in transient binding interactions. The disorder to order transition, which occurs during binding interactions in disordered regions, renders the interaction highly reversible while maintaining the high specificity. The enrichment of intrinsic disorder in date hubs may facilitate transient interactions, which might be required for date hubs to interact with different partners at different times. Proteins 2007. © 2006 Wiley‐Liss, Inc.
Temperature and pressure dependence of carrier recombination processes in GaAsSb/GaAs quantum well lasers
Authors: Hild Konstanze , Sweeney Stephen J. , Marko Igor P. , Jin Shirong R. , Johnson Shane R. , Chaparro Sergio A. , Yu Shuiqing , Zhang Yong‐Hang
Published: December 2006

We investigated the temperature and pressure dependence of carrier recombination processes occurring in GaAsSb edge‐emitting lasers operating near 1.3 μm. Below ∼100 K, the threshold current, I th, is dominated by the radiative current, I rad, and is proportional to temperature, T. However, above 100 K, non‐radiative recombination increases abruptly such that by 125 K it accounts for 40% of I th. From high pressure measurements at this temperature, we find that the non‐radiative current decreases with increasing pressure, consistent with the presence of Auger recombination. At room temperature, non‐radiative recombination accounts for ∼90% I th and gives rise to a super‐linear temperature dependence of I th, in spite of the fact that I rad ∝ T. At room temperature the non‐radiative current increases with increasing pressure, indicating that under ambient operating conditions, the devices are also limited by carrier leakage into the Γ‐minimum of the GaAs barriers and possibly also into the X‐minima of the GaAsP confining layers. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Carrier recombination mechanisms in mid‐infrared GaInAsSb quantum well lasers
Authors: O'Brien K. , Sweeney S. J. , Adams A. R. , Jin S. R. , Ahmad C. N. , Murdin B. N. , Salhi A. , Rouillard Y. , Joullié A.
Published: December 2006

Hydrostatic pressure and spontaneous emission techniques have been used to examine the important recombination mechanisms in type‐I GaInAsSb/GaSb quantum well lasers. High pressure results indicate that Auger recombination dominates the threshold current of 2.11 μm and 2.37 μm devices and is the origin of their temperature sensitivity around room temperature. While the characteristics of the 2.37 μm devices are much improved by the suppression of the CHSH Auger process, since its spin–orbit splitting energy is greater than its band gap, other important Auger processes such as CHHL and CHCC persist. In the larger band gap 2.11 μm devices, an increase in threshold current with pressure is observed suggesting that CHSH Auger is present in these devices at atmospheric pressure and contributes to performance degradation at these shorter wavelengths. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Tuning of the high‐brightness tapered laser and its applications
Authors: Bohdan R. , Bercha A. , Mariani O. , Wojdak M. , Dybala F. , Adamiec P. , Trzeciakowski W. , Weber J. , Kelemen M. T.
Published: December 2006

Tapered lasers offer high beam quality together with high power. Wavelength tunability is therefore a valuable feature for such laser, making it a compact alternative for e.g. Titanium‐Sapphire laser. We demonstrate the combination of fine tuning by grating (in the 30 nm range) with the coarse tuning by pressure (up to 12 kbar) for a high power tapered laser emitting around 960 nm at ambient pressure. At the fixed current of 1.5 A the laser was tuned in a 100 nm range (from 980 nm to 880 nm) emitting between 200 mW and 300 mW with high quality of the beam.

We examined the possibility of using pressure‐tuned tapered laser diodes in spectroscopy and we demonstrated high spatial resolution for photocurrent and photoreflectance measurements. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Artificial neural network‐based hysteresis estimation of capacitive pressure sensor
Authors: Dibi Zohir , Lamine Hafiane M.
Published: December 2006

The output of the Capacitive Pressure Sensor (CPS) depends both on the input pressure and on its recent history, an effect called hysteresis. A Switched Capacitor Interface (SCI) converts and amplifies either the change in capacitance of pressure‐sensor into an equivalent voltage and the difference between the input pressure due to the hysteresis effect. A new approach to CPS modeling based on artificial neural network (ANN) is proposed taken into account the dynamic environment in which the temperature variation is quite large and the response characteristics of a CPS are highly nonlinear and temperature dependent. The first model is used to simulate the behaviour of the CPS. The second model is based on inverse modeling, which can be used to compensate the hysteresis effect the temperature drift and the nonlinearity. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Pressure dependence of Raman modes in DWCNT filled with PbI2 semiconductor
Authors: González J. , Power Ch. , Belandria E. , Broto J. M. , Puech P. , Sloan J. , Flahaut E.
Published: December 2006

Unpolarized Raman spectra of tangential modes on DWNTs filled with 1D nanocrystalline PbI2 semiconductor excited with 647 nm were studied at room temperature and elevated pressure up to 30 GPa. The tangential optical phonon modes of the carbon nanotubes are sensitive to the in plane stress and split into a contribution associated with the external and internal tube. Up to 11 GPa we find a pressure coefficient for the internal tube of 3.7 cm–1 GPa–1 and for the external tube of 6.3 cm–1 GPa–1. In addition, the tangential band of the external tubes broadens and decreases in amplitude. The corresponding Raman features of the internal tubes appear to be considerably less sensitive to pressure. In the range 11 to 15 GPa we observed a discontinuity in the slope (red shift) of the pressure dependence of the frequency of the tangential modes. This phase transition is associated to a possible structural distortion of the nanotube cross‐section. When increasing the pressure furthermore up to 30 GPa the pressure coefficients for the tangential modes associated to the internal and external tubes are the same (10.6 cm–1 GPa–1). All findings lead to the conclusion that the outer tubes act as a protection shield fore the inner tubes (at least up to 11 GPa). (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Ab initio study of double‐wall carbon nanotubes under uniaxial pressure
Authors: Fagan Solange B. , Lemos V.
Published: December 2006

Ab initio calculations were performed in (5,5)@(10,10) double‐wall carbon nanotubes subjected to external forces applied in the radial direction. The inner tubes were found to be less sensitive to pressure than the outer tubes. The electronic band structure was preserved practically unchanged for uniaxial pressures up to 1 GPa. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Raman spectroscopy of single‐walled carbon nanotubes at high pressure: Effect of interactions between the nanotubes and pressure transmitting media
Authors: Proctor J. E. , Halsall M. P. , Ghandour A. , Dunstan D. J.
Published: December 2006

We have studied single‐walled carbon nanotubes (SWNT) at high pressure using Raman spectroscopy, in a variety of common solvents as hydrostatic pressure‐transmitting media. We find that the response of the Raman G‐band to high pressure varies significantly with choice of solvent. In particular, with hexane we observe a new irreversible effect – a flat Raman response to 0.7 GPa. We draw tentative conclusions from this work – that the solvents used can penetrate the interstitial spaces between nanotubes in a bundle and, following the approach of Amer et al. [1], that absorption of the pressure‐transmitting media plays a role in the response of the SWNTs to high pressure. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interaction of a methanol molecule with C60 under pressure
Authors: Lemos V. , Guerini S. , Abreu R. F. , Mendes Filho J. , Fagan Solange B.
Published: December 2006

The interaction between a C60 molecule with methanol, the main composition of the currently employed pressure transmitting fluid was studied. The simulations include C60 under hydrostatic or uniaxial pressure interacting with methanol. The relaxed structure as well as the binding energies and the electronic density of states were obtained. The analysis of binding energy indicates that the methanol molecule is attracted to C60 under hydrostatic pressure, while repulsed if the pressure is uniaxial. The results establish that the mechanisms of interaction between this nanometer scale system and the medium may change during the compression. Density of states results indicate severe changes in the Raman spectrum of the system under compression. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)