bluuebunny/crossref_metadata_2025 huggingface dataset:
Incorporating hidden Markov models for identifying protein kinase‐specific phosphorylation sites
Authors: Huang Hsien‐Da , Lee Tzong‐Yi , Tzeng Shih‐Wei , Wu Li‐Cheng , Horng Jorng‐Tzong , Tsou Ann‐Ping , Huang Kuan‐Tsae
Published: May 2005

Protein phosphorylation, which is an important mechanism in posttranslational modification, affects essential cellular processes such as metabolism, cell signaling, differentiation, and membrane transportation. Proteins are phosphorylated by a variety of protein kinases. In this investigation, we develop a novel tool to computationally predict catalytic kinase‐specific phosphorylation sites. The known phosphorylation sites from public domain data sources are categorized by their annotated protein kinases. Based on the concepts of profile Hidden Markov Models (HMM), computational models are trained from the kinase‐specific groups of phosphorylation sites. After evaluating the trained models, we select the model with highest accuracy in each kinase‐specific group and provide a Web‐based prediction tool for identifying protein phosphorylation sites. The main contribution here is that we have developed a kinase‐specific phosphorylation site prediction tool with both high sensitivity and specificity. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1032–1041, 2005
Gene products with evolutionary functions
Authors: Arber Werner
Published: May 2005

It is often tacitly assumed that all gene products serve the needs of life functions of the individual carrying the genome. However, a close look at the formation of genetic variations, which are the drivers of biological evolution, reveals a different view. While a majority of the products of genes, such as housekeeping genes and genes essential for each individual, when exposed to particular life conditions respond to the definition given above, other gene products clearly carry out evolutionary functions at the level of populations. Products of these evolution genes act as generators of genetic variations and/or as modulators of the frequency of genetic variation. This is most readily seen with bacterial populations. Many different mechanisms contribute to the occasional, overall formation of genetic variations. These mechanisms can be grouped into three mechanistically and qualitatively different strategies of generating genetic variations. In addition to the activities of evolution genes, specific properties of matter such as tautomery also contribute to the formation of genetic variations. The views that nature cares actively for biological evolution are documented by evidence taken mainly from microbial genetics. Essential elements of the theory of molecular evolution are discussed, as well as the relevance of this theory for higher organisms and its impact on our worldview.
Structural analysis of a highly acetylated protein using a curved‐field reflectron mass spectrometer
Authors: Wang Dongxia , Thompson Paul , Cole Philip A. , Cotter Robert J.
Published: May 2005

Matrix‐assisted laser desorption/ionization mass spectrometry and tandem mass spectrometry (MS/MS) were used to determine the multiple acetylation sites in the histone acetyltransferase (HAT): p300‐HAT. Partial cleavage of the peptides containing acetylated lysine residues by trypsin provided a set of nested sequences that enabled us to determine that multiple acetylation occurs on the same molecule. At the same time, cleavages resulting in a terminal unacetylated lysine suggested that not all of these sites are fully modified. Using MS and MS/MS, we were able to characterize both the unmodified and acetylated tryptic peptides covering more than 82% of the protein.
Two‐stage affinity purification for inducibly phosphorylated membrane proteins
Authors: Peirce Matthew J. , Begum Shajna , Saklatvala Jeremy , Cope Andrew P. , Wait Robin
Published: May 2005

Characterisation of tyrosine phosphorylations induced in immune cells in response to inflammatory stimuli may help elucidate the molecular bases of the diversity of immune responses. We have used anti‐phosphotyrosine antibodies in combination with cell surface biotinylation in a two‐step affinity purification procedure to recover pervanadate‐induced tyrosine phosphorylated proteins from sub‐cellular compartments, including the cell surface, of murine T cells and macrophages prior to separation by solution‐phase isoelectric focussing and one‐dimensional gel electrophoresis and identification by tandem mass spectrometry.
Quantitative analysis of protein expression using amine‐specific isobaric tags in Escherichia coli cells expressing rhsA elements
Authors: Aggarwal Kunal , Choe Leila H. , Lee Kelvin H.
Published: May 2005

We describe the use of amine‐specific isobaric tags for protein expression quantification to study the effect of rhsA element over‐expression in Escherichia coli. The use of an isobaric tagging strategy facilitates a shotgun approach to proteomic analysis and enables quantitation of up to four samples in parallel, based on the reporter ion series using tandem mass spectrometry (MS/MS). Using a liquid chromatography matrix‐assisted laser desorption/ionization approach, 23 139 MS/MS spectra were collected. Five thousand sixty‐three peptides derived from 780 proteins were quantified including several lower abundance proteins, such as transcription factors, DnaB and DnaG. More than 65% of the proteins had at least two high confidence peptide matches per protein (p < 0.05). Further, a statistical test based on the Grubb's and Rosner's tests was able to discriminate outlier data. The removal of outlier data had no significant effect on the functional categories of proteins that were represented in the study.
Improvements in two‐dimensional gel electrophoresis by utilizing a low cost “in‐house” neutral pH sodium dodecyl sulfate‐polyacrylamide gel electrophoresis system
Authors: Graham David R. M. , Garnham Christopher P. , Fu Qin , Robbins Jeffrey , Van Eyk Jennifer E.
Published: May 2005

Two‐dimensional gel electrophoresis (2‐DE) is widely used for initial protein separation in proteomics. Commercial products using neutral pH sodium dodecyl sulfate‐polyacrylamide gel electrophoresis ((SDS‐PAGE)/(Bis (2‐hydroxyethyl) imino‐tris (hydroxymethyl) methane‐HCl, or Bis‐Tris)) have greatly improved this technique, but cost and limited sizes restrict their applications. An “in‐house” system is presented, resulting in better resolution, separation, and new spot visualization and improved resolution when compared to Tris‐HCl gels. Their utility is demonstrated using albumin‐depleted serum samples, rabbit heart left ventricle, and human immunodeficiency virus type 1 (HIV‐1).
Acrylamide‐agarose copolymers: Improved resolution of high molecular mass proteins in two‐dimensional gel electrophoresis
Authors: Roncada Paola , Cretich Marina , Fortin Riccardo , Agosti Susanna , De Franceschi Lucia , Greppi Gian Franco , Turrini Francesco , Carta Franco , Turri Stefano , Levi Marinella , Chiari Marcella
Published: May 2005

A method was developed in order to analyse high molecular mass proteins by two‐dimensional (2‐D) electrophoresis using a copolymer of acrylamide and allyl agarose instead of Bis cross‐linked polyacrylamide (PA) gels in sodium dodecyl sulphate‐electrophoresis. In this work, the matrix composition was optimised to improve the resolution of proteins larger than 200 kDa. The new gel type does not entrap large proteins and protein complexes at the application site. Mechanical properties were investigated through rheological measurements, which suggested the formation of a highly entangled elastomeric soft gel. A high 2‐D resolution of proteins, extracted from membranes of red blood cells, was obtained in these gels. An example of tryptic digestion, peptide extraction and matrix‐assisted laser desorption/ionisation‐time of flight mass spectrometry was reported. The results demonstrate that the new gel is fully compatible with mass spectrometry protein analysis.
A quantitative proteomic approach using two‐dimensional gel electrophoresis and isotope‐coded affinity tag labeling for studying human 20S proteasome heterogeneity
Authors: Froment Carine , Uttenweiler‐Joseph Sandrine , Bousquet‐Dubouch Marie‐Pierre , Matondo Mariette , Borges Jean‐Philippe , Esmenjaud Charlotte , Lacroix Christelle , Monsarrat Bernard , Burlet‐Schiltz Odile
Published: May 2005

Mammalian proteasomes are macromolecular complexes formed of a catalytic 20S core associated to two regulatory complexes. The 20S core complex consists of four stacked rings of seven α or β subunits. Three β subunits contain a catalytic site and can be replaced by three interferon γ‐inducible counterparts to form the immunoproteasome. Cells may constitutively possess a mixture of both 20S proteasome types leading to a heterogeneous proteasome population. Purified rat 20S proteasome has been separated in several chromatographic fractions indicating an even higher degree of complexity in 20S proteasome subunit composition. This complexity may arise from the presence of subunit isoforms, as previously detected in purified human erythrocyte 20S proteasome. In this study, we have used a quantitative proteomic approach based on two‐dimensional gel electrophoresis and isotope‐coded affinity tag (ICAT™) labeling to quantify the variations in subunit composition, including subunit isoforms, of 20S proteasomes purified from different cells. The protocol has been adapted to the analysis of low quantities of 20S proteasome complexes. The strategy has then been validated using standard proteins and has been applied to the comparison of 20S proteasomes from erythrocytes and U937 cancer cells. The results obtained show that this approach represents a valuable tool for the study of 20S proteasome heterogeneity.
Novel polystyrene‐supported zirconocene catalyst for olefin polymerization and its catalytic kinetics
Authors: Wang Wenqin , Wang Li , Wang Jianfeng , Wang Jianjun , Ma Zhenli
Published: May 2005

Through the Diels–Alder reaction between cyclopentadiene groups attached to polystyrene in the presence of zirconocene, novel polystyrene‐supported metallocene catalysts were prepared. A novel method for immobilizing metallocene catalysts was investigated, and the resultant polystyrene‐supported metallocene for olefin polymerization was studied. The results of olefin polymerization showed that different crosslinking degrees of support in the catalyst system had significant effects on the catalytic behavior. The influence of the [Al]/[Zr] molar ratio and the temperature on the (co)polymerization activity was studied. When 1‐hexene and 1‐dodecene were used for copolymerization with ethylene, an obvious positive comonomer effect was observed. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 2650–2656, 2005
Novel catalyst system of MCl2/FeCl3·6H2O/PPh3 (M = Ni, Co, or Mn) for the atom transfer radical polymerization of methyl methacrylate
Authors: Jian Cao , Chen Jin , Zhang Keda
Published: May 2005

MCl2 (M = Ni, Co, Sn, or Mn) and PPh3 together acted as a catalyst for the radical polymerization of methyl methacrylate (MMA) in the presence of ethyl 2‐bromoisobutyrate as an initiator. The four systems all led to conventional radical polymerizations, which yielded polymers with a weight‐average molecular weight/number‐average molecular weight (Mw/Mn) ratio greater than 2.0 and became well controlled when a certain amount of FeCl3·6H2O was added. The polymerizations of MMA catalyzed by these four FeCl3‐modified catalyst systems provided well‐defined polymers with low polydispersities (Mw/Mn < 1.28). © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 2625–2631, 2005
Copolymers of 2,5‐bis[(4‐methoxyphenyl) oxycarbonyl]styrene with styrene and methyl methacrylate: Synthesis, monomer reactivity ratios, thermal properties, and liquid crystalline behavior
Authors: Zhao Yong‐feng , Yi Yi , Fan Xinghe , Chen Xiaofang , Wan Xinhua , Zhou Qi‐Feng
Published: May 2005

Copolymers of a liquid crystalline monomer, 2,5‐bis[(4‐methoxyphenyl)oxycarbonyl]styrene (MPCS), with St and MMA were prepared by free radical polymerization at low conversion in chlorobenzene with 2,2′‐azobisisobutyronitrile (AIBN) as initiator. The copolymers of poly(MPCS‐co‐St) and poly(MPCS‐co‐MMA) were characterized by 1H NMR and GPC. The monomer reactivity ratios were determined by using the extended Kelen–Tudos (EKT) method. Structural parameters of the copolymers were obtained from the possibility statistics and monomer reactivity ratios. The influence of MPCS content in copolymers on the glass transition temperatures of copolymers was investigated by DSC. The thermal stabilities of the two copolymer systems increased with an increase of the molar fraction of MPCS in the copolymers. The liquid crystalline behavior of the copolymers was also investigated using DSC and POM. The results revealed that the copolymers with high MPCS molar contents exhibited liquid crystalline behaviors. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 2666–2674, 2005
Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry study on copolymers obtained by the alternating copolymerization of bis(γ‐lactone) and epoxide with potassium tert‐butoxide
Authors: Zhang Chenxi , Ochiai Bungo , Endo Takeshi
Published: May 2005

Oligomer samples obtained by the anionic copolymerization of a bis(γ‐lactone), 2,8‐dioxa‐1‐methylbicyclo[3.3.0]octane‐3,7‐dione (1), and glycidyl phenyl ether with potassium tert‐butoxide have been analyzed by matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectrometry. The MALDI‐TOF mass spectra of these cooligomers show well‐resolved signals that can be reliably assigned to linear, alternating cooligomers that have carboxylate chain ends or alkoxide chain ends and cyclic ones. The formation of these three series of cooligomers suggests that the polymerization process involves concomitant intermolecular transesterification and intramolecular back‐biting. The intramolecular back‐biting reaction causes the formation of cyclic cooligomers, whereas the intermolecular transesterification causes the reduction of the molecular weight and the transformation of the alkoxide active chain end into a carboxylate chain end. The MALDI‐TOF mass spectrometry study has shown that an excess of monomer 1 enhances the selectivity of propagation by increasing the probability of the attack of the alkoxide chain end to 1. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 2643–2649, 2005
Synthesis and swelling behavior of comb‐type grafted hydrogels by reversible addition–fragmentation chain transfer polymerization
Authors: Liu Qunfeng , Zhang Ping , Lu Mangeng
Published: May 2005

The comb‐type grafted hydrogels poly(N‐isopropylacrylamide)‐g‐poly(N‐isopropylacrylamide) (PNIPAM‐g‐PNIPAM) and poly(acrylic acid)‐g‐poly(N‐isopropylacrylamide) (PAAc‐g‐PNIPAM) were prepared by reversible addition–fragmentation chain transfer polymerization. A macromolecular chain‐transfer agent was prepared first. Then, hydrogels were obtained by a reaction with a comonomer (N‐isopropylacrylamide or acrylic acid) in the presence of N,N‐methylenebisacrylamide as a crosslinker. The equilibrium swelling ratios and the swelling and deswelling kinetics of PNIPAM‐g‐PNIPAM were measured. The effects of the chain length and amount on the swelling behavior were investigated. The deswelling mechanism was illustrated. Meanwhile, the PAAc‐g‐PNIPAM hydrogel was used to confirm the versatility of this novel method. It was prepared in an alcoholic medium, whereas hydrogen‐bonding complexes formed in 1,4‐dioxane, which was chosen as the reaction medium for the PNIPAM‐g‐PNIPAM hydrogel. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 2615–2624, 2005
Self‐assembly of GaAs holed nanostructures by droplet epitaxy
Authors: Wang Zhiming M. , Holmes Kyland , Shultz John L. , Salamo Gregory J.
Published: May 2005

We report on Ga nano‐droplets on GaAs(100) that are not stable under arsenic flux. Spontaneous evolution in shape leads to many interesting GaAs nanostructures. GaAs nano‐crystals shaped like lighted candles and square‐holed round coins are observed under different growth conditions. The underlying physics of the formation of these interesting nano‐structures can be understood in terms of GaAs growth under a uniform arsenic flux and a non‐uniform Ga supply from the Ga nano‐droplets. These novel shaped GaAs nanostructures, in an AlGaAs matrix, offer promising applications in optoelectronics. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Transport of excitation energy in a molecular aggregate. VIII. Numerical simulation of exciton processes in thylakoid membrane
Authors: Panda Anirban , Datta Sambhu N.
Published: May 2005

We investigate the exciton dynamics in a molecular crystal. The dynamics is based on the exciton Hamiltonian, the phonon Hamiltonian, and the exciton–phonon interaction linear in phonon coordinates. Using the interaction picture, expressions were previously obtained for the rate of coherent migration of the exciton clothed by phonons, and the rate of incoherent or hopping motion. In this work we derive an expression for the clothed exciton propagator, which permits an explicit calculation of the hopping rate. Thus, the rates of exciton generation, coherent transfer, and hopping are determined completely from theory. These velocity constants, along with the experimental fluorescence decay constants and reaction rate constants for the excited molecules, are used to write a generalized master equation that describes the rate of change of exciton population at each site. The master equation can be numerically solved by using a time step of the order of a few femtoseconds, while the excited‐state reactions and exciton transfer occur in the picosecond scale. Exciton dynamics is numerically simulated for a simple model of thylakoid membrane in green plants. The model is based on the known characteristics of thylakoid architecture. The membrane is divided into 97 zones, each zone in the bulk containing 1,442 chlorophylls, one P700, and one P680. The latter two pigments are randomly placed in each zone, while keeping their distance between 55 and 60 Å. This accounts for the randomness in orientation. The disorder of the chlorophyll molecules within the domains of photosystems is neglected. Our findings are as follows. On average, about 6 million photons within the range of 655–681 nm pass through a membrane in 1 s. About 2.3% of incident photons are absorbed by the membrane chlorophyll molecules. For an excitation bandwidth of 70–175 cm−1, the coherent transfer rate between two adjacent molecules is 1.138 ± 0.488 ps−1. Because the Debye frequency is expected to be much smaller, the slow phonon limit applies. The exciton–phonon coupling constant that can be determined from the transition dipole–transition dipole interaction model leads to a hopping rate of 0.088 ps−1 at 300 K. A steady state is effectively achieved for each zone in the bulk in ∼5 ns. After a period of 50 ns, P700 and P680 in average trap at the rate of 650–702 and 629–679 excitons per second, respectively. The average rate of charge separation and subsequent reactions of each excited photosystem varies as 592–639 per second for PSI and 630–680 per second for PSII. These numbers lead to a reasonable estimate for the amount of glucose produced in each square meter of leaf area in a day. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Quadratic Padé approximants and the intruder state problem of multireference perturbation methods
Authors: Perrine Trilisa M. , Chaudhuri Rajat K. , Freed Karl F.
Published: May 2005

Simple and quadratic Padé resummation methods are applied to high‐order series from multireference many‐body perturbation theory (MR‐MBPT) calculations using various partitioning schemes (Møller–Plesset, Epstein–Nesbet, and forced degeneracy) to determine their efficacy in resumming slowly convergent or divergent series. The calculations are performed for the ground and low‐lying excited states of (i) CH2, (ii) BeH2 at three geometries, and (iii) Be, for which full configuration interaction (CI) calculations are available for comparison. The 49 perturbation series that are analyzed include those with oscillatory and monotonic divergence and convergence, including divergences that arise from either frontdoor or backdoor intruder states. Both the simple and quadratic Padé approximations are found to speed the convergence of slowly convergent or divergent series. However, the quadratic Padé method generally outperforms the simple Padé resummation. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
The surface chemistry of heterogeneous catalysis: Mechanisms, selectivity, and active sites
Authors: Zaera Francisco
Published: May 2005

The role of chemical kinetics in defining the requirements for the active sites of heterogeneous catalysts is discussed. A personal view is presented, with specific examples from our laboratory to illustrate the role of the chemical composition, structure, and electronic properties of specific surface sites in determining reaction activity and selectivity. Manipulation of catalytic behavior via the addition of chemical modifiers and by tuning of the reaction conditions is also introduced. © 2005 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 5: 133–144; 2005: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.20040
Monolayer‐derivative functionalization of non‐oxidized silicon surfaces
Authors: Shirahata Naoto , Hozumi Atsushi , Yonezawa Tetsu
Published: May 2005

This article describes a variety of monolayers anchored directly onto silicon surfaces without an oxide interlayer, their formation mechanisms, their technological applications, and our personal views on the future prospects for this field. The chemical modification of non‐oxidized silicon surfaces utilizing monolayers was first reported in 1993. The basic finding that a non‐oxidized silicon surface could be neutralized with alkyl chains through direct covalent linkage, i.e., silicon–carbon, has offered chemical scientists ease of handling even in an ambient environment and, thus, research has been predictably focused on forming anti‐stiction coating films for nano‐ and micro‐electromechanical systems (NEMS/MEMS). Such surface reforming has also been achieved by using other monolayers, which form interfacial bonds, e.g., silicon–nitrogen and silicon–oxygen. The resultant monolayer surfaces are useful for silicon‐based applications including molecular electron transfer films, monolayer templates, molecular insulators, capsulators, and bioderivatives. Such monolayers are applicable not only for surface modification, but also for manipulating individual nanomaterials. By modifying the terminal groups of monolayers with nanomaterials including nanocrystals and biomolecules, the nanomaterials can remarkably be immobilized directly onto non‐oxidized silicon surfaces based on the formation mechanisms of the monolayer. Such immobilizations will revolutionize the analysis of the specific features and capabilities of individual nanomaterials. Furthermore, the path will be opened for the development of more advanced monolayer‐derived chip technology. To achieve this goal, it is extremely important to thoroughly understand the functionalization processes on silicon, since the resultant internal structures and properties of monolayer‐derivative silicon may strongly depend on their course of formation. © 2005 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 5: 145–159; 2005: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.20041
Dual substrate recognition of aminotransferases
Authors: Hirotsu Ken , Goto Masaru , Okamoto Akihiro , Miyahara Ikuko
Published: May 2005

Pyridoxal 5′‐phosphate‐dependent aminotransferases reversibly catalyzes the transamination reaction in which the α‐amino group of amino acid 1 is transferred to the 2‐oxo acid of amino acid 2 (usually 2‐oxoglutarate) to produce the 2‐oxo acid of amino acid 1 and amino acid 2 (glutamate). An aminotransferase must thus be able to recognize and bind two kinds of amino acids (amino acids 1 and 2), the side chains of which are different in shape and properties, from among many other small molecules. The dual substrate recognition mechanism has been discovered based on three‐dimensional structures of aromatic amino acids, histidinol phosphate, glutamine : phenylpyruvate, acetylornithine, and branched‐chain amino acid aminotransferases. There are two representative strategies for dual substrate recognition. An aromatic amino acid aminotransferase prepares charged and neutral pockets for acidic and aromatic side chains, respectively, at the same place by a large‐scale rearrangement of the hydrogen‐bond network caused by the induced fit. In a branched‐chain aminotransferase, the same hydrophobic cavity implanted with hydrophilic sites accommodates both hydrophobic and acidic side chains without side‐chain rearrangements of the active‐site residues, which is reminiscent of the lock and key mechanism. Dual substrate recognition in other aminotransferases is attained by combining the two representative methods. © 2005 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 5: 160–172; 2005: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.20042
A study of PIXE continuum polarization properties
Authors: Potiriadis C. , Karydas A. G. , Zarkadas Ch. , Clouvas A.
Published: May 2005

The continuum radiation emitted after the proton bombardment of a solid or gaseous target can be described mainly by three mechanisms: the secondary electron bremsstrahlung (SEB), the quasi‐free electron bremsstrahlung (QFEB) and the atomic bremsstrahlung (AB). Each background mechanism exhibits a different relative contribution in the PIXE continuum according to the projectile energy, the x‐ray region and the atomic number of the target element. The anisotropy of the SEB and AB continuum, peaking at 90° with respect to the beam axis, has been confirmed and studied experimentally in the past. In the present work, the degree of polarization of the PIXE continuum was determined experimentally in the energy region 3–5 keV for a solid, thick carbon target and for 2.5 and 3 MeV proton energies. Copyright © 2005 John Wiley & Sons, Ltd.
Combined micro‐PIXE facility and monochromatic cathodoluminescence spectroscopy applied to colored minerals of natural stones: an example from amazonite
Authors: Vaggelli Gloria , Borghi Alessandro , Cossio Roberto , Fedi Mariaelena , Fiora Laura , Giuntini Lorenzo , Massi Mirko , Olmi Filippo
Published: May 2005

Quantitative micro‐PIXE and cathodoluminescence spectra obtained for amazonite crystals from Malawi and Brazil granitoids, in order to check the trace elements presumably responsible for their color. These granitoids, used as Natural Stones for inside coverings and furnishings, are precious and rare, and owe their preciousness to the color of the rock‐forming aquamarine amazonite. The trace elements investigated by means of micro‐PIXE show the occurrence of Fe, Rb, Pb and Ga at concentrations above the minimum detection limit. In particular, the Malawi amazonite has a higher Pb content than the Brazil amazonite, but for Pb content both samples show a nearly flat pattern profile along the whole crystals. The cathodoluminescence spectra in both samples display three main peaks at 284, 558 and 680 nm which may be attributed to the presence of Pb2+, Mn2+ and Fe3+, respectively. As no Mn was detected by PIXE we suggest that its occurrence is below the PIXE detection limit. Micro‐PIXE analysis and cathodoluminescence spectra of most common and uncolored K‐feldspars do not reveal the presence of lead; therefore we support the hypothesis of Pb as the chromophore source. Copyright © 2005 John Wiley & Sons, Ltd.
Micro‐PIXE characterization of different skin models
Authors: Gontier E. , Barberet P. , Barbotteau Y. , Gáspár K. , Habchi C. , Hunyadi J. , Incerti S. , Kiss B. , Mavon A. , Moretto P. , Pouthier T. , Rosdy M. , Surlève‐Bazeille J. E. , Ynsa M. D.
Published: May 2005

Because of the large natural inter‐individual variability and of some difficulties in obtaining material from surgery or from healthy volunteers, the use of human native skin in experimentation comes up against fierce competition from experimental models, such as reconstituted epidermis or human skin grafted in animals. In this study, micro‐PIXE was used in association with other ion beam microanalysis techniques to characterize different epidermis models on a microscopic scale. The ionic species were found to be highly compartmentalized in the different strata of human skin with a distribution that can be explained in the frame of the homeostatic barrier function. Reconstituted epidermis obtained from airlifted culture, epidermis of mice foot sole and human forehead skin grafts transplanted into mice are the models investigated and compared with human native skin. Very similar inorganic ion patterns were observed in all epidermis, suggesting comparable permeability barrier mechanisms and validating their use as alternative approaches to native skin experimentation. In the near future, we plan to use some of these models in penetration studies and for investigating effects of exposure to different environmental stresses. Copyright © 2005 John Wiley & Sons, Ltd.
Rapid chemical state analysis in air by highly sensitive high‐resolution PIXE using a v. Hamos crystal spectrometer
Authors: Maeda Kuniko , Hasegawa Kenichi , Maeda Masaru , Ogiwara Kiyoshi , Hamanaka Hiromi
Published: May 2005

A high‐resolution PIXE system composed of a curved crystal and a position‐sensitive proportional counter in v. Hamos geometry was constructed for rapid chemical state analysis in air. Data processing software to measure the time variation of PIXE spectra was installed in the system. The system was applied to obtain time‐resolved spectra of sulfur Kβ on the minute time‐scale. Time‐dependent variation of the fine structure was recognized clearly in the S Kβ spectra obtained from marine sediment samples. Copyright © 2005 John Wiley & Sons, Ltd.
Towards a semantics-based information theory
Authors: Baumann Peter
Published: May 2005

We develop a formal framework to give computer programs an abstract interpretation as information transformers. Then the quantitative relation between input and output information is investigated. Our theory is based on
information domains
, a refinement of the classical domains used in denotational semantics, and on the theory of abstract interpretation of functional languages.
Context induction: A proof principle for behavioural abstractions and algebraic implementations
Authors: Hennicker Rolf
Published: May 2005

An induction principle, called context induction, is presented which is appropriate for the verification of behavioural properties of abstract data types. The usefulness of the proof principle is documented by several applications: the verification of behavioural theorems over a behavioural specification, the verification of behavioural implementations and the verification of “forget-restrict-identify” implementations.

In particular, it is shown that behavioural implementations and “forget-restrict-identify” implementations (under certain assumptions) can be characterised by the same condition on contexts, i.e. (under the given assumptions) both concepts are equivalent. This leads to the suggestion to use context induction as a uniform proof method for correctness proofs of algebraic implementations.
A proof system for communicating processes with value-passing
Authors: Hennessy M.
Published: May 2005

A proof system for a version of CCS with value-passing is proposed in which the reasoning about data is factored out from that about the structure of processes. The system is shown to be sound and complete for finite terms with respect to a denotational semantics based on Acceptance Trees.
Reconstruction of the thumb and digit by toe to hand transplantation
Authors: Chen Zhong Wei , Chen Zheng Rong
Published: May 2005

Since the rapid development of microsurgery it is feasible to replant most severed thumbs and digits. In certain patients, however, the trauma is so severe that replantation cannot be performed, such as crush or burst injuries where the amputated part is badly smashed or broken into pieces. There are many methods used to reconstruct amputated thumbs or digits. In our hospital reconstruction of the thumb is accomplished by second toe transplantation, nail flap of the great toe transplantation and bone graft, and nail flap of the great toe and skeleton from the second toe transplantation. Reconstruction of fingers is undertaken through second toe transplantation and second and third toe transplantation. After total loss of the hand, double second toe transplant is used for reconstruction.
Emergency repair and reconstruction in the severely crushed hand
Authors: De S. Das , Tai Lee Soon , Pho Robert W. H.
Published: May 2005

Crushing injuries of the hand are a common clinical problem which require judgement and assessment by an experienced hand surgeon for an optimum result. The crushed hand has to be viewed in the perspective of injury to an essential organ with its skin and contents, namely muscles, vessels, nerves, tendons, bone and joints. A poor result is often due to inadequate wound debridement, failure to identify the extent of crushing of the devitalized tissue, closure of the skin under tension in the presence of wound contamination, and complex repairs in an avascular bed. In an emergency situation, the simplest suitable procedure is preferred. Open degloving injuries, grease and paint gun injuries, and especially closed crushing, degloving injuries can be very misleading and need special attention.
Open approach in pancreatic and infected pancreatic necrosis: Laparostomies and preplanned revisions
Authors: Függer Reinhold , Schulz Franz , Rogy Michael , Herbst Friedrich , Mirza Darius , Fritsch Arnulf
Published: May 2005

One hundred and two patients with acute necrotizing pancreatitis were treated in accordance with a combined regimen of necrosectomy, open drainage by laparostomies, and repeated re‐explorations. The severity of pancreatitis was assessed by the APACHE II score (median 15 on admission). Eighty‐seven (85%) patients were classified as having infected pancreatic necrosis and only 15 (15%) as having pancreatic necrosis. Overall, 36 (35%) patients died, most of multiple organ failure. Survival was significantly impaired by bacterial contamination of pancreatic necrosis (p=0.008),bacteremia (p=0.0001)and infected bronchial secretions (p=0.05).The mortality rate was reduced from 53% to 28% by changing the regimen of re‐explorations from on demand to regular 48 hour intervals. Despite the fact that open packing was associated with a high frequency of gastrointestinal fistulas (30%), this concept seems to be a successful and recommendable approach in the therapy of pancreatic and infected pancreatic necrosis.
Hyperthermo‐chemotherapy combined with cytoreductive surgery for the treatment of gastric cancer with peritoneal dissemination
Authors: Yonemura Yutaka , Fujimura Takashi , Fushida Sachio , Takegawa Shigeru , Kamata Toru , Katayama Kanji , Kosaka Takeo , Yamaguchi Akio , Miwa Kouichi , Miyazaki Ituo
Published: May 2005

Continuous hyperthermic peritoneal perfusion (CHPP) with anticancer agents (mitomycin C and cisplatin) in warm saline was performed in patients with peritoneal dissemination of gastric cancer following resection of the primary lesion. The effect of CHPP was examined by a second‐look operation. This study includes 41 cases of gastric cancer with peritoneal dissemination but without liver metastasis treated during the past 6 years. The overall median survival was 14.6 months to 64.2 months from CHPP to death and the 3‐year survival rate was 28.5%. Second look surgery revealed a remarkable diminution in the degree of peritoneal dissemination in 7 (50%) of 14 patients with disappearance of ascites after only one course of CHPP in 7 (77.8%) of 9 patients. Long‐term 3 year‐survival was noted in 4 (9.8%) patients on CHPP. Side effects were renal insufficiency in 2 (5%) patients, leukopenia in 2 (5%) patients, and perforation of the small intestine in 1 (2%) patient. These results suggest the effectiveness of CHPP in the treatment of gastric cancer with peritoneal dissemination.
Secondary hyperparathyroidism: Diagnosis of site of recurrence
Authors: Casanova Daniel , Sarfati Emile , De Francisco Angel , Amado J. Antonio , Arias Manuel , Dubost Claude
Published: May 2005

Persistent or recurrent hyperparathyroidism after total parathyroidectomy with forearm implant may be caused by hyperplastic grafted tissue, residual parathyroid tissue left in the neck or the presence of a supernumerary gland not found during surgery. A correct assessment of graft function is needed to localize the source of hormone excess and to avoid an unnecessary neck reoperation in cases of graft dependent hyperparathyroidism. In 12 patients with relapsing hyperparathyroidism after total parathyroidectomy with forearm implant, total ischemic blockade of the arm bearing the parathyroid graft produced a “transitory implantectomy” with a significant reduction of serum levels of intact PTH in those with graft hyperfunction. In 6 patients with proved supernumerary glands, total ischemia of the graft was not followed by significant changes in intact PTH. Hyperparathyroidism was reversed after surgical resection of the parathyroid implants in the 6 patients with positive responses to the ischemic maneuver. A repeat neck reoperation removing cervical or mediastinal supernumerary glands was followed by control of recurrent hyperparathyroidism in the 6 patients with a negative response to the ischemic blockade. Total ischemic blockade of the arm bearing the parathyroid graft is a valuable new method for a correct assessment of graft function after total parathyroidectomy with forearm autotransplantation.
Use of Ligasure in Thyroidectomy Procedures: Results of a Prospective Comparative Study
Authors: Kirdak Turkay , Korun Nusret , Ozguc Halil
Published: May 2005

The thyroidectomy procedure requires many manupulations to achieve prompt hemostasis. This study assessed whether the outcomes of thyroidectomy using the Ligasure electrothermal vessel sealer were comparable with the conventional suture‐ligation technique. We prospectively evaluated 58 consecutive patients who underwent thyroidectomy. Patients were allocated into two groups according to their preference. There were 30 patients in the Ligasure group and 28 patients in the conventional surgery group. Complications, operating time, and hospital stay were compared between the two groups and suture‐ligations performed in the Ligasure group were recorded. The age, sex, and indications were similar in the two groups (p > 0.05). Complication rates and hospital stays did not show any difference according to the techniques used. Operating time was shorter in the hemithyroidectomy and total thyroidectomy patients of the Ligasure group (mean ± SD: 77.38 ± 13.71 vs. 99.80 ± 12.53 minutes, p = 0.005; and 102.50 ± 16.69 vs.128.89 ± 19.74 minutes, p = 0.010). The mean ± SD number of suture‐ligations for each patient in the Ligasure group was 1.83 ± 2.12. Thyroid surgery using the Ligasure is safe, and its complication rates are comparable to these found with the conventional surgical technique. Use of the Ligasure during hemithyroidectomy and total tyhroidectomy operations provides a significantly shorter operating time.
Introducing the Cardibra: A Randomised Pilot Study of a Purpose Designed Support Bra for Women Having Cardiac Surgery
Authors: Naismith Carolyn , Street Annette
Published: May 2005

Background: Cardiac nurses instruct women to wear a brassiere (bra) after a sternotomy for cardiac surgery to reduce lateral tension on the wound. However this practice is rarely implemented because regular bras impede nursing care in the immediate postoperative period. The Cardibra was developed to address the inadequacies of the regular bra and provide an alternate method of breast support.

Aim: To develop a purpose designed support bra (the Cardibra) and evaluate its effectiveness on sternal wound healing and the reduction of pain for women who had a sternotomy for cardiac surgery.

Methods: The study consisted of two stages. Stage 1 described the development of the Cardibra. Stage 2 was a pilot study of a clinical trial, prospective, randomised two-group design. The treatment group consisted of 10 women using the Cardibra immediately following surgery and the control group of 10 who wore a regular bra 3 days post surgery. Repeated measures at six time points assessed pain levels and wound healing.

Results: This study indicated that the Cardibra might have beneficial therapeutic effects on pain levels and wound healing up to day 14 after cardiac surgery.

Conclusion: This innovative device may offer therapeutic benefits to women following cardiac surgery.
Compensatory regulation among ER chaperones in C. elegans
Authors: Kapulkin Vadim , Hiester Brian G. , Link Christopher D.
Published: May 2005

We have identified a particularly clear case of compensatory transcriptional regulation among ER chaperones in Caenorhabditis elegans using a GFP reporter transgene that is under the control of the promoter of hsp‐4, a C. elegans homolog of GRP‐78/BiP. Knockdown by RNA interference of 9 known or predicted ER chaperones induced hsp‐4 upregulation via the ire‐1/xbp‐1 signaling cascade employed in the unfolded protein response. We show that this compensatory regulation is specific for ER chaperones, not dependent on RNA interference, and required for maintaining viability in worms containing a deletion of the hsp‐3 gene.
Ammonia displaces methanol bound to the water oxidizing complex of photosystem II in the S2 state
Authors: Evans Michael C.W. , Ball Richard J. , Nugent Jonathan H.A.
Published: May 2005

Ammonia and methanol both bind to the water oxidising complex of photosystem II during its turnover, possibly at sites where water binds during the normal water oxidation process. We have investigated the interaction between these two water analogues at the S2 state of the water oxidising cycle using electron magnetic resonance techniques. We find evidence that ammonia displaces methanol from its binding site.
Obstructive sleep apnea and head and neck neoplasms
Authors: Rada Roy
Published: May 2005

OBJECTIVE

To elaborate the relationship between obstructive sleep apnea (OSA) and head and neck neoplasms (HNN).

STUDY DESIGN AND SETTING

A systematic review of the MEDLINE literature.

RESULTS

Thirty of 34 articles indexed under OSA and HNN were about neoplasms that presented first as OSA. Four of the articles were about treatment of HNN causing OSA and gave incidences varying from 8% to 92%. Quality of life surveys confirm that patients with malignant HNN have sleep problems. Xerostomia may contribute to these sleep problems, and the role of salivary mucins deserves consideration.

CONCLUSIONS

This review of the literature raises several new research questions about the clinical and biological relationships between OSA and HNN. (Otolaryngol Head Neck Surg 2005;132:794‐9.)
Seldinger‐assisted videotelescopic intubation (SAVI): A common sense approach to the difficult pediatric airway
Authors: Michaelson Peter G. , Mairy Eric A.
Published: May 2005

OBJECTIVES

To describe the Seldinger‐assisted videotelescopic intubation (SAVI) technique, a complementary method for aiding in difficult pedi‐atric intubations that uses common equipment available to the practicing otolaryngologist.

STUDY DESIGN

Technique description.

METHODS

Detailed description of technique for use of a pediatric laryngoscope with video‐assisted endotracheal tube (ETT) covered rigid tracheoscopy controlled intubation in difficult pediatric airways.

RESULTS

In our practice, SAVI is vital in establishing a secure airway in the difficult‐to‐intubate child. After insertion of a laryngoscope, an appropriate sized endotracheal tube is delivered through the glottis under direct video‐visualization from a rigid telescope using a variation of the well‐established Seldinger technique. The telescope serves as the stable ETT stylet that also provides panoramic visualization. The ETT slides over the telescope to provide a secure airway directly visible to all in the operating room. Benefits of the SAVI technique to previously described video‐assisted intubations with flexible or specially designed endoscope devices include decreased cost, employment of previously existing endoscopy skills, the benefit of rigid delivery of the endotracheal tube as well as innate versatility to a multitude of clinical situations.

CONCLUSIONS

The SAVI technique offers an additional practical clinical solution to the difficult pediatric airway. Although ultimately establishing the airway depends on the skills of the operator, the SAVI technique has saved multiple lives by using common equipment through a common‐sense approach. EBM rating: D. (Otolaryngol Head Neck Surg 2005;132:677‐680.)
Long‐term histological outcomes of injected autologous fat into human vocal folds after secondary laryngectomy
Authors: Sasai Hisanori , Watanabe Yusuke , Muta Hiroshi , Yoshida Junichi , Hayashi Ibuki , Ogawa Makoto , Kubo Takeshi
Published: May 2005

OBJECTIVE

To histologically evaluate the long‐term outcomes of autologous fat grafts after injection laryngoplasty in the human larynx.

STUDY DESIGN AND SETTING

We injected liposuctioned fat for vocal fold augmentation in patients with vocal fold paralysis. We suctioned autologous fat from the low abdomen with an 18‐G disposable needle and a 20‐mL disposable syringe under negative pressure. This is different from the conventional liposuction technique and avoids the use of special equipment. In this article, we report the histological evaluation of 2 patients (patient 1: 12 months, patient 2: 41 months) who required total laryngectomy after autologous fat injection into the vocal folds.

RESULTS

Histological examination revealed normal‐appearing viable adipocytes with minimal inflammatory response in both patients.

CONCLUSIONS

Our liposuctioned autologous fat injection histologically offered long‐term improvement in patients with impaired glottal closure from vocal fold paralysis. (Otolaryngol Head Neck Surg 2005;132:685‐688.)