bluuebunny/crossref_metadata_2025 huggingface dataset:
Coupled lattice‐Boltzmann and finite‐difference simulation of electroosmosis in microfluidic channels
Authors: Hlushkou Dzmitry , Kandhai Drona , Tallarek Ulrich
Published: August 2004

In this article we are concerned with an extension of the lattice‐Boltzmann method for the numerical simulation of three‐dimensional electroosmotic flow problems in porous media. Our description is evaluated using simple geometries as those encountered in open‐channel microfluidic devices. In particular, we consider electroosmosis in straight cylindrical capillaries with a (non)uniform zeta‐potential distribution for ratios of the capillary inner radius to the thickness of the electrical double layer from 10 to 100. The general case of heterogeneous zeta‐potential distributions at the surface of a capillary requires solution of the following coupled equations in three dimensions: Navier–Stokes equation for liquid flow, Poisson equation for electrical potential distribution, and the Nernst–Planck equation for distribution of ionic species. The hydrodynamic problem has been treated with high efficiency by code parallelization through the lattice‐Boltzmann method. For validation velocity fields were simulated in several microcapillary systems and good agreement with results predicted either theoretically or obtained by alternative numerical methods could be established. Results are also discussed with respect to the use of a slip boundary condition for the velocity field at the surface. Copyright © 2004 John Wiley & Sons, Ltd.
Accuracy analysis of super compact scheme in non‐uniform grid with application to parabolized stability equations
Authors: Esfahanian V. , Ghader S. , Ashrafi Kh.
Published: August 2004

A brief derivation of the super compact finite difference method (SCFDM) in non‐uniform grid points is presented. To investigate the accuracy of the SCFDM in non‐uniform grid points the Fourier analysis is performed. The Fourier analysis shows that the grid aspect ratio plays a crucial role in the accuracy of the SCFDM in a non‐uniform grid. It is also found that the accuracy of the higher order relations of the SCFDM is more sensitive to grid aspect ratio than the lower order relations. In addition, to obtain a mathematical representation of the accuracy and making clear the role of the aspect ratio in the accuracy of the SCFDM in non‐uniform grids, the modified equation approach is used. For the sake of demonstrating the analytical results obtained from the Fourier analysis and the modified equation approach, the super compact finite difference method is applied to solve the Blasius boundary layer and the non‐linear parabolized stability equations as numerical examples indicating the difficulty with non‐uniform grid spacing using the super compact scheme. Copyright © 2004 John Wiley & Sons, Ltd.
From cells to tissues: Fluorescence confocal microscopy in the study of histological samples
Authors: Transidico Pietro , Bianchi Marco , Capra Maria , Pelicci Pier Giuseppe , Faretta Mario
Published: August 2004

Our knowledge of the genetic mechanisms controlling cell proliferation and differentiation usually originates from in vitro cultured cell line models. However, the definition of the molecular switches involved in control of homeostasis and the understanding of the changes occurring in neoplastic transformation require looking at single cells as the components of a complex tissue network. Histological examination of tissue samples can gain a substantial amount of information from high‐resolution fluorescence analysis. In particular, confocal microscopy can help in the definition of functional pathways using multiparameter analysis. In this report, we present acquisition and analysis procedures to obtain high‐resolution data from tissue sections. Confocal microscopy coupled to computational restoration, statistical evaluation of spatial correlations, and morphological analysis over large tissue areas were applied to colorectal samples providing a molecular fingerprint of the biological differences inferred from classical histological examination. Microsc. Res. Tech. 64:89–95, 2004. © 2004 Wiley‐Liss, Inc.
Improvement in volume estimation from confocal sections after image deconvolution
Authors: Difato F. , Mazzone F. , Scaglione S. , Fato M. , Beltrame F. , Kubínová L. , Janáček J. , Ramoino P. , Vicidomini G. , Diaspro A.
Published: August 2004

The confocal microscope can image a specimen in its natural environment forming a 3D image of the whole structure by scanning it and collecting light through a small aperture (pinhole), allowing in vivo and in vitro observations. So far, the confocal fluorescence microscope (CFM) is considered a true volume imager because of the role of the pinhole that rejects information coming from out‐of‐focus planes. Unfortunately, intrinsic imaging properties of the optical scheme presently employed yield a corrupted image that can hamper quantitative analysis of successive image planes. By a post‐image collection restoration, it is possible to obtain an estimate, with respect to a given optimization criterium, of the true object, utilizing the impulse response of system or Point Spread Function (PSF). The PSF can be measured or predicted so as to have a mathematical and physical model of the image‐formation process. Further modelling and recording noise as an additive Gaussian process has used the regularized Iterative Constrained Tykhonov Miller (ICTM) restoration algorithm for solving the inverse problem. This algorithm finds the best estimate iteratively searching among the possible positive solutions; in the Fourier domain, such an approach is relatively fast and elegant. In order to compare the effective improvement in the quantitative image information analysis, we measured the volume of reference objects before and after image restoration, using the isotropic Fakir method. Microsc. Res. Tech. 64:151–155, 2004. © 2004 Wiley‐Liss, Inc.
Adaptive image‐processing technique and effective visualization of confocal microscopy images
Authors: Sun Yinlong , Rajwa Bartek , Robinson J. Paul
Published: August 2004

A common observation about confocal microscopy images is that lower image stacks have lower voxel intensities and are usually blurred in comparison with the upper ones. The key reasons are light absorption and scattering by the objects and particles in the volume through which light passes. This report proposes a new technique to reduce such noise impacts in terms of an adaptive intensity compensation and structural sharpening algorithm. With these image‐processing procedures, effective 3D rendering techniques can be applied to faithfully visualize confocal microscopy data. Microsc. Res. Tech. 64:156–163, 2004. © 2004 Wiley‐Liss, Inc.
Backscattered light confocal imaging of intracellular MTT‐formazan crystals
Authors: Bernas Tytus , Dobrucki Jurek W.
Published: August 2004

Metabolically active animal and plant cells reduce MTT tetrazolium salt to a corresponding nonfluorescent formazan. Reduction of MTT by viable cells is exploited in a number of tests widely used in biological research. The aim of this study was to optimize a microscopy method of detecting small crystals of MTT‐formazan formed in intact cells maintained in in vitro cultures. We examined scattering properties of small intracellular crystals of MTT formazan and found that the efficiency of light scattering was dependent on wavelength. Small (<3 μm) crystals of MTT‐formazan, formed in viable cells, scattered red, but not blue, light. Large crystals, which are formed later at a stage when cells begin to lose viability, scattered both red and blue light. We conclude that optimal detection of early stages of crystallization of MTT‐formazan in living cells is possible using confocal microscopy of red, but not blue, scattered light. High contrast and resolution of images can be achieved by filtering out interference effects in the frequency domain. Microsc. Res. Tech. 64:126–134, 2004. © 2004 Wiley‐Liss, Inc.
Saturation modified point spread functions in two‐photon microscopy
Authors: Cianci Gianguido C. , Wu Jianrong , Berland Keith M.
Published: August 2004

Excitation saturation can dramatically alter the effective imaging point spread function (PSF) in two‐photon fluorescence microscopy. The saturation‐modified PSF can have important implications for resolution in fluorescence imaging as saturation leads to both an increased fluorescence observation volume and an altered spatial profile for the PSF. We introduce here a computational approach to accurately quantify molecular excitation profiles that represent the modified imaging PSF in two‐photon microscopy under the influence of excitation saturation. An analytical model that accounts for pulsed laser excitation is developed to calculate the influence of saturation at any location within the excitation laser profile. The overall saturation modified molecular excitation profiles are then evaluated numerically. Our results demonstrate that saturation can play an important role in two‐photon fluorescence microscopy even with relatively modest excitation levels. Microsc. Res. Tech. 64:135–141, 2004. © 2004 Wiley‐Liss, Inc.
Three‐dimensional microscopy migrates to the web with “PowerUp Your Microscope”
Authors: Bonetto Paola , Boccacci Patrizia , Scarito Marco , Davolio Mirko , Epifani Mattia , Vicidomini Giuseppe , Tacchetti Carlo , Ramoino Paola , Usai Cesare , Diaspro Alberto
Published: August 2004

“PowerUp Your Microscope” is a software package designed and realized for the optimization of 3D optical microscopy image quality using the Internet and inverse problems computational approaches. The package is mainly devoted to 3D microscopy users, being operative for wide‐field, confocal, and multiphoton microscopy. It provides the microscopy community with an extremely easy and comparatively powerful access to advanced image restoration methods. The core of the computational section is the optical system modeling and inverse deconvolution implementation, which is strongly linked to Web‐based software and technology. This project constitutes a real and effective migration to the Web, extending computational approaches to image restoration to the whole microscopy user community, regardless of their background. Microsc. Res. Tech. 64:196–203, 2004. © 2004 Wiley‐Liss, Inc.
Liquid chromatography coupled to nuclear magnetic resonance spectroscopy for the identification of isoflavone glucoside malonates in T. pratense L. leaves.
Authors: de Rijke Eva , de Kanter Frans , Ariese Freek , Brinkman Udo A. Th. , Gooijer Cees
Published: August 2004

Previous studies revealed that the main isoflavones in extracts of leaves of T. pratense L. are biochanin A and formononetin, their 7‐O‐glucosides, and two glucoside malonate isomers of each of them. Since LC–MS(/MS) did not provide sufficient information to distinguish the glucoside malonate isomers, in the present paper LC–NMR as well as off‐line two‐dimensional NMR were used to obtain further structural information. Matrix solid‐phase dispersion (MSPD) was applied to obtain sufficiently high analyte concentrations to perform LC–NMR. Stop‐flow reversed‐phase LC–NMR was performed using a gradient of deuterated water and deuterated acetonitrile. Off‐line COSY and NOESY experiments were carried out to determine the positions of the glucose moiety on the flavonoid aglycone, and of the malonate moiety on the glucose. Based on the fragmentation patterns in MS/MS and the NMR spectra, the two formononetin glucoside malonate isomers were identified as 7‐O‐β‐D‐glucoside 6´´‐O‐malonate and 7‐O‐β‐D‐glucoside 4´´‐O‐malonate; i.e. they only differ in the substitution position of the malonate group on the glucoside ring. The biochanin A glucoside malonate isomers, however, have quite different structures. The main and later eluting isomer is biochanin A 7‐O‐β‐D‐glucoside 6´´‐O‐malonate, and the minor and earlier eluting isomer is 5‐hydroxy‐7‐methoxyisoflavone 4´‐O‐β‐D‐glucoside 4´´‐O‐malonate: the positions of the methoxy group and the glucoside 6´´‐O‐malonate group on the flavonoid skeleton are interchanged.
Degrees of d. c. e. reals
Authors: Downey Rod , Wu Guohua , Zheng Xizhong
Published: August 2004

A real α is called a c. e. real if it is the halting probability of a prefix free Turing machine. Equivalently, α is c. e. if it is left computable in the sense that L(α) = {q ∈ ℚ : q ≤ α} is a computably enumerable set. The natural field formed by the c. e. reals turns out to be the field formed by the collection of the d. c. e. reals, which are of the form α—β, where α and β are c. e. reals. While c. e. reals can only be found in the c. e. degrees, Zheng has proven that there are Δ02 degrees that are not even n‐c. e. for any n and yet contain d. c. e. reals, where a degree is n‐c. e. if it contains an n‐c. e. set. In this paper we will prove that every ω‐c. e. degree contains a d. c. e. real, but there are ω + 1‐c. e. degrees and, hence Δ02 degrees, containing no d. c. e. real. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Weak computability and representation of reals
Authors: Zheng Xizhong , Rettinger Robert
Published: August 2004

The computability of reals was introduced by Alan Turing [20] by means of decimal representations. But the equivalent notion can also be introduced accordingly if the binary expansion, Dedekind cut or Cauchy sequence representations are considered instead. In other words, the computability of reals is independent of their representations. However, as it is shown by Specker [19] and Ko [9], the primitive recursiveness and polynomial time computability of the reals do depend on the representation. In this paper, we explore how the weak computability of reals depends on the representation. To this end, we introduce three notions of weak computability in a way similar to the Ershov's hierarchy of Δ02‐sets of natural numbers based on the binary expansion, Dedekind cut and Cauchy sequence, respectively. This leads to a series of classes of reals with different levels of computability. We investigate systematically questions as on which level these notions are equivalent. We also compare them with other known classes of reals like c. e. and d‐c. e. reals. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Spaces allowing Type‐2 Complexity Theory revisited
Authors: Schröder Matthias
Published: August 2004

The basic concept of Type‐2 Theory of Effectivity (TTE) to define computability on topological spaces (X, τ) or limit spaces (X,→) are representations, i. e. surjection functions from the Baire space ontoX. Representations having the topological property of admissibility are known to provide a reasonable computability theory. In this article, we investigate several additional properties of representations which guarantee that such representations induce a reasonable Type‐2 Complexity Theory on the represented spaces. For each of these properties, we give a nice characterization of the class of spaces that are equipped with a representation having the respective property. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Some recent developments on Shannon's General Purpose Analog Computer
Authors: Silva Graça Daniel
Published: August 2004

This paper revisits one of the first models of analog computation, the General Purpose Analog Computer (GPAC). In particular, we restrict our attention to the improved model presented in [11] and we show that it can be further refined. With this we prove the following: (i) the previous model can be simplified; (ii) it admits extensions having close connections with the class of smooth continuous time dynamical systems. As a consequence, we conclude that some of these extensions achieve Turing universality. Finally, it is shown that if we introduce a new notion of computability for the GPAC, based on ideas from computable analysis, then one can compute transcendentally transcendental functions such as the Gamma function or Riemann's Zeta function. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Some subrecursive versions of Grzegorczyk's Uniformity Theorem
Authors: Skordev Dimiter
Published: August 2004

A theorem published by A. Grzegorczyk in 1955 states a certain kind of effective uniform continuity of computable functionals whose values are natural numbers and whose arguments range over the total functions in the set of the natural numbers and over the natural numbers. Namely, for any such functional a computable functional with one function‐argument and the same number‐arguments exists such that the values of the first of the functionals at functions dominated by a given one are completely determined by their restrictions to numbers not exceeding the corresponding values of the second functional at the given function. We prove versions of this theorem for the class of the primitive recursive functionals and for the class of the elementary recursive ones. Analogous results can be proved for many other subrecursive classes of functionals. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Fold zone analysis in wiping die bending process by using experimental and numerical approaches
Authors: Mkaddem Ali , Potiron Alain
Published: August 2004

This paper deals with an analysis of the fold zone of bent parts within the sheet thickness by means of micro hardness measurement and numerical modelling. The failure risk has to be accurately predicted by using a continuum damage mechanics in order to avoid some expensive experiments. In this reason, a 3D numerical model, based on Lemaitre damage formulations, has been developed. The scalar damage variable D as well as the hardening law are taken to be isotropic within the sheet. The numerical approach is based on an incremental integration scheme of the constitutive equations coupled with ductile damage and von Mises criteria. The corresponding numerical algorithm is implemented into ABAQUS/Standard code. During bending operation, the damage variable evolution is computed and the hydrostatic stress effect is investigated within the sheet thickness. The hardening and plastic strain evolutions have been compared with the micro hardness one deduced from experimental tests. The comparison between experimental and numerical results illustrates the capability of the model in 3D process simulation, particularly in bending processes. Copyright © 2004 John Wiley & Sons, Ltd.
Application of piece‐wise linear weight functions for 2D 8‐node quadrilateral element in contact problems
Authors: Luo Chouping , Klisinski Marek
Published: August 2004

The present study is a continuation of our previous work with the aim to reduce problems caused by standard higher order elements in contact problems. The difficulties can be attributed to the inherent property of the Galerkin method which gives uneven distributions of nodal forces resulting in oscillating contact pressures. The proposed remedy is use of piece‐wise linear weight functions. The methods to establish stiffness and/or mass matrix for 8‐node quadrilateral element in 2D are presented, i.e. the condensing and direct procedures. The energy and nodal displacement error norms are also checked to establish the convergence ratio. Interpretation of calculated contact pressures is discussed. Two new 2D 8‐node quadrilateral elements, QUAD8C and QUAD8D, are derived and tested in many examples, which show their good performance in contact problems. Copyright © 2004 John Wiley & Sons, Ltd.
Cancer incidence among children in France, 1990–1999
Authors: Desandes Emmanuel , Clavel Jacqueline , Berger Claire , Bernard Jean‐Louis , Blouin Pascale , de Lumley Lionel , Demeocq François , Freycon Fernand , Gembara Piotr , Goubin Aurélie , Le Gall Edouard , Pillon Pascale , Sommelet Danièle , Tron Isabelle , Lacour Brigitte
Published: August 2004

Background

Cancer is the second most important cause of death for children aged less than 15 years in France, unintentional injuries being the leading cause. The aim of the present study was to estimate the incidence of childhood cancer from six Childhood Cancer Registries covering 32% of France.

Procedure

Incident cancer cases diagnosed between 1990 and 1999 in children (0–14 years) resident in the administrative areas covered by each Registry were included. Annual age‐standardized rates (ASRs) were adjusted by the world population. The estimated annual percent change (EAPC) was used to measure trend towards changes in the annual age‐standardized incidence rate.

Results

With 4234 registered cases, the ASRs per million children were 137.5 for all cancers combined, 42.3 for leukemia, 29.1 for central‐nervous‐system tumors, 15.6 for lymphomas, 14.1 for sympathetic‐nervous‐system tumors, and 9.1 for renal tumors. The ASR of all cancers combined was slightly higher in males (145.8 per million children) than in females (128.7 per million children) with an M/F ratio of 1.2. No significant incidence trend was observed, with an EAPC of +0.2% [IC 95% (−2.5; +3.0); P = 0.89].

Conclusions

The estimated incidence rates are similar to those reported in previous studies in European and North American countries. These results will contribute to the development of National Registration of Childhood Cancer in France and support the national research program on childhood cancer. © 2004 Wiley‐Liss, Inc.
Interferon‐γ sensitizes osteosarcoma cells to fas‐induced apoptosis by up‐regulating fas receptors and caspase‐8
Authors: Inaba Hiroto , Glibetic Maria , Buck Steven , Ravindranath Yaddanapudi , Kaplan Joseph
Published: August 2004

Background

Osteosarcoma is the third most frequent neoplasm in adolescents. Although chemotherapy, frequently used in pre‐ and post‐operative settings, has resulted in significant improvement in disease‐free survival, some patients show little sensitivity to chemotherapy and alternative therapeutic strategies are needed. Because the Fas ligand/Fas receptor (CD95, APO‐1) apoptosis pathway is a potential therapeutic target in osteosarcomas, we examined the effect of IFN‐γ on Fas‐induced apoptosis in four osteosarcoma cell lines.

Procedure and Results

As measured by flow cytometry, all cell lines expressed cell surface IFN‐γ receptors, and when cultured for 2 days in the presence of IFN‐γ, all cell lines exhibited a significant increase in expression of Fas receptors. By flow cytometric detection of intracellular fragmented DNA as a marker of apoptosis, all cell lines cultured with either IFN‐γ or anti‐Fas antibody (clone CH‐11) alone showed only moderate apoptosis, whereas significantly high levels of apoptosis occurred in cells cultured with both IFN‐γ and CH‐11. Western blotting analysis also revealed that IFN‐γ caused up‐regulation of caspase‐8 in all cell lines, but no change in Fas‐associated death domain protein (FADD/MORT1) or caspase‐3. Both caspase‐8 and caspase‐3 were activated when apoptosis was induced with both IFN‐γ and CH‐11. Addition to cultures of z‐IETD‐fmk, an inhibitor of caspase‐8, significantly blocked this apoptosis.

Conclusions

IFN‐γ sensitizes osteosarcoma cells to Fas‐induced apoptosis through up‐regulation of Fas receptor and caspase‐8. Combined immunotherapy with IFN‐γ and either anti‐Fas monoclonal antibody or cytotoxic T cells that bear Fas ligand might be a useful adjunctive therapy for patients with osteosarcoma. © 2004 Wiley‐Liss, Inc.
A New clinical score for disease activity in Langerhans cell histiocytosis
Authors: Donadieu Jean , Piguet C. , Bernard F. , Barkaoui M. , Ouache M. , Bertrand Y. , Ibrahim H. , Emile J.F. , Hermine O. , Tazi A. , Genereau T. , Thomas C.
Published: August 2004

Objective

To develop an objective tool for assessing disease activity in patients with Langerhans cell histiocytosis (LCH).

Method

Scoring system was developed and applied to a database containing information on 612 patients.

Results

At diagnosis, the score distribution was highly asymmetrical: the score was between 0 and 2 in 74% of cases, 3–6 in 16%, 7–10 in 3%, and more than 10 in 6%. The 5‐year mortality rates were 1, 4.4, and 43.4%, respectively, among patients with initial scores of 0–2, 3‐6, and >6. Stability or an increase of the score at 6 weeks was highly predictive of death among patients with initial scores above 6, while score stability had no significant impact on vital outcome among patients with low or moderate scores at diagnosis.

Conclusions

This LCH disease activity score provides an objective tool for assessing disease severity, both at diagnosis and during follow‐up and treatment. © 2004 Wiley‐Liss, Inc.
Rapid screening of highly efficient vaccine candidates by immunoproteomics
Authors: Chen Zijun , Peng Bo , Wang Sanying , Peng Xuanxian
Published: August 2004

Diseases caused by microorganisms can be controlled by vaccines, which require neutralizing antigens. Therefore, it is very important to identify highly efficient immunogens for immune prevention. By combining immunoproteomics and bacterial challenge after immunization, we developed a rapid method for screening protected antigens of pathogenic bacteria in aquaculture. Our approach may be divided into three consecutive steps. First, dominant immunogens of outer membrane proteins are screened by immunoproteomics. Second, proteins with the ability to induce production of neutralizing antibodies are identified from the immunogens by virulent bacterium challenge following vaccination. Third, vaccine candidates are determined by evaluation of neutralizing abilities. Information on the candidates has been obtained for further gene cloning by mass spectrometry. Our results indicate that highly efficient protected antigens were identified from the outer membrane proteome of Aeromonas hydrophila, in which an immunogen showed 71.4% protective ability with multivalent functions to A. hydrophila and Aeromonas sobria. In summary, we have developed a high‐throughout, accurate, rapid and highly efficient method which will play an active role in immune prevention for microbiological diseases.
Mass spectrometric protein structure characterization reveals cause of migration differences of haptoglobin α chains in two‐dimensional gel electrophoresis
Authors: Mikkat Stefan , Koy Cornelia , Ulbrich Markus , Ringel Bruno , Glocker Michael O.
Published: August 2004

Haptoglobin belongs to the major constituents of plasma and acts as hemoglobin‐binding and acute‐phase protein. Due to the occurrence of three major allelic variants and further structural modifications, the α chains of haptoglobin form varying spot patterns in two‐dimensional gel electrophoresis (2‐DE) gels, which is generally observed in differential proteome analyses using plasma or related body fluids of humans. In the present study plasma samples from 10 donors of initially unknown haptoglobin phenotype were separated by 2‐DE and tryptic digests of excised haptoglobin α chain spots were analyzed by matrix‐assisted laser desorption/ionization time of flight mass spectrometry (MALDI‐TOF‐MS) and MALDI‐quadrupole ion trap TOF‐MS. Haptoglobin α1S, α1F, as well as α2 chains were found to occur each with at least three structurally differing protein species: (i) the unmodified form, which corresponds to the sequence database entries; (ii) derivatives, in which asparagine at position five is deamidated to aspartic acid; and (iii) derivatives with an additional C‐terminal arginine residue. These structural variants account for the most commonly observed spot patterns of haptoglobin α chains in Coomassie‐stained gels. Additionally, a minor derivative of the haptoglobin α2 chain carrying both modifications, deamidation at position five and the C‐terminal arginine residue, was identified. Theoretical pI values of the characterized structural variants are, consistent with their observed migration in the 2‐DE gels.
Proteomics‐based identification of novel Candida albicans antigens for diagnosis of systemic candidiasis in patients with underlying hematological malignancies
Authors: Pitarch Aida , Abian Joaquín , Carrascal Montserrat , Sánchez Miguel , Nombela César , Gil Concha
Published: August 2004

Systemic candidiasis remains a major cause of disease and death, particularly among patients suffering from hematological malignancies. In an attempt to contribute to the discovery of useful biomarkers for its diagnosis and therapeutic monitoring, we embarked on a mapping of Candida albicans immunogenic proteins specifically recognized by antibodies produced during the natural course of systemic Candida infection in this high‐risk population. About 85 immunoreactive protein species were detected with systemic candidiasis patients' serum specimens by using immunoproteomics (i.e., two‐dimensional electrophoresis followed by Western blotting), and identified through a combination of peptide mass fingerprinting by matrix‐assisted laser desorption/ionization‐time of flight‐mass spectrometry (MALDI‐TOF‐MS), de novo peptide sequencing using nano‐electrospray ionization‐ion trap (ESI‐IT) MS, and genomic database searches. This proteomic approach has led to the characterization of 42 different housekeeping enzymes as C. albicans antigens. Their biological significance is also discussed. Furthermore, this study is the first to report that 26 of them exhibit antigenic properties in C. albicans, and 35 of them become targets of the human antibody response to systemic candidiasis. Our findings suggest that the production of antibodies to C. albicans phosphoglycerate kinase and alcohol dehydrogenase during systemic candidiasis could be associated with a differentiation of the human immune response. We also highlight the relationship between changes in maintenance of circulating levels of specific anti‐Candida antibodies and patients' outcome. Some of these variations, especially the rise of high anti‐enolase antibody concentrations, appear to be related to recovery from systemic candidiasis in these patients, which might serve as markers for predicting their outcome. This approach could therefore provide new challenges for diagnosis and clinical follow‐up of these fungal infections, and even for antifungal drug or vaccine design.
CFP10 discriminates between nonacetylated and acetylated ESAT‐6 of Mycobacterium tuberculosis by differential interaction
Authors: Okkels Limei Meng , Müller Eva‐Christina , Schmid Monika , Rosenkrands Ida , Kaufmann Stefan H. E. , Andersen Peter , Jungblut Peter R.
Published: August 2004

ESAT‐6 (the 6 kDa early secreted antigenic target) protein species in short‐term culture filtrate of Mycobacterium tuberculosis were separated in a 4–5 narrow range pI gradient two‐dimensional gel electrophoresis (2‐DE). Eight ESAT‐6 protein species were analyzed in detail by peptide mass fingerprinting matrix‐assisted laser desorption/ionization‐mass spectrometry as well as by electrospray ionization‐tandem mass spectrometry. An N‐terminal Thr acetylation was identified in four species and a C‐terminal truncation was identified in two species. In 2‐DE blot overlay assays, the recombinant 10 kDa culture filtrate protein (CFP10) discriminated N‐terminal acetylated and nonacetylated ESAT‐6 by differential interaction, whereas removal of the C‐terminal 11 residues of ESAT‐6 had no effects thereon. This example shows that the access to the protein species level can be a prerequisite to understand regulation of protein‐protein interaction.
A comprehensive proteome map of growing Bacillus subtilis cells
Authors: Eymann Christine , Dreisbach Annette , Albrecht Dirk , Bernhardt Jörg , Becher Dörte , Gentner Sandy , Tam Le Thi , Büttner Knut , Buurman Gerrit , Scharf Christian , Venz Simone , Völker Uwe , Hecker Michael
Published: August 2004

The proteome of growing cells of Bacillus subtilis was analyzed in order to provide the basis for its application in microbial physiology. DNA arrays were used to calculate the number of genes transcribed in growing cells. From the 4100 B. subtilis genes, 2515 were actively transcribed in cells grown under standard conditions. From these genes 1544 proteins should be covered by our standard gel system pI 4–7. Using this standard gel system and supplementary zoom gels (pI 5.5–6.7, 5–6, 4.5–5.5, and 4–5) 693 proteins which are expressed in growing cells were detected that cover more than 40% of the vegetative proteome predicted for this region. Particularly broad coverage and thus comprehensive monitoring will be possible for central carbohydrate metabolism (glycolysis, pentose phosphate shunt, and citric acid cycle), amino acid synthesis pathways, purine and pyrimidine metabolism, fatty acid metabolism, and main cellular functions like replication, transcription, translation, and cell wall synthesis. Comparing the theoretical pI and Mr values with those experimentally determined a reasonable correlation was found for the majority of protein spots. By a color code outliers with dramatic deviations in charge or mass were visualized that may indicate post‐translational modifications. In addition to the cytosolic neutral and alkaline proteins, 130 membrane proteins were found relying on sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE) separation in combination with electrospray ionization‐tandem mass spectrometry (ESI‐MS/MS) techniques. The vegetative proteome containing 876 proteins in total is now ready for physiological applications. Two main proteome fractions (pI 4–7 and zoom gel pI 4.5–5.5) should be sufficient for such high‐throughput physiological proteomics.
Action and Reaction: Chlamydophila pneumoniae proteome alteration in a persistent infection induced by iron deficiency
Authors: Wehrl Wolfgang , Meyer Thomas F. , Jungblut Peter R. , Müller Eva‐Christina , Szczepek Agnes J.
Published: August 2004

Chlamydophila pneumoniae is an obligate intracellular pathogen implicated in a variety of acute and chronic diseases. Long‐term infections are associated with a persistent life stage, in which bacteria can stay for years. They are less accessible to antibiotic treatment but still prone to sustain an inflammatory response. Different in vitro models have been established to mimic and characterize chlamydial persistency. For C. pneumoniae and Chlamydia trachomatis, altered metabolic activities and changed antigenic profiles compared to acute infections have been reported. Most studies including transcriptome and proteome analyses describe persistency induced by IFNγ treatment. Here, we use iron depletion of the infected cell culture that also leads into persistent infection. We describe differently regulated proteins found by subtractive proteome analysis comparing two early stages of infection with and without addition of the iron chelator deferoxamine‐mesylate. While only one bacterial protein was up‐regulated during iron deficiency up to 24 h post infection (p.i.), 11 were found to be up‐regulated and eight to be down‐regulated from 24–48 h p.i. Two down‐regulated proteins could be identified by peptide mass fingerprinting as thioredoxin reductase and chromosome partitioning protein (ParB). The latter is involved in chromosome segregation. Thus, using a comparative approach we identified on a proteome level down‐regulation of ParB in persistent chlamydial forms, which is in agreement with previous results describing changes in cell division and atypical altered morphology of persistent Chlamydiae.
Amphiphilic maleic acid‐containing alternating copolymers—2. Dilute solution characterization by light scattering, intrinsic viscosity, and PGSE NMR spectroscopy
Authors: Sauvage E. , Plucktaveesak N. , Colby R.H. , Amos D.A. , Antalek B. , Schroeder K.M. , Tan J.S.
Published: August 2004

The dilute solution behavior of several alternating copolymers of maleic acid has been characterized by static and dynamic light scattering, intrinsic viscosity, and pulsed‐gradient spin‐echo NMR spectroscopy. The copolymer of maleic acid–sodium salt and isobutylene (IBMA‐Na, Mw ∼350 kg/mol) dissolves readily in concentrated aqueous salt solutions. Changes in chain dimensions with ionic strength and pH are similar to those of the lesser salt solution‐soluble poly(acrylic acid‐sodium salt). The hydrophobically modified (with n‐butyl, n‐hexyl, n‐octyl, and phenethyl amines) copolymers of maleic acid–sodium salts and isobutylene (IBMA‐NHR‐Na) show no sign of large intermolecular aggregation in 0.1 N sodium acetate (NaAc). However, the sizes of the copolymers are relatively small compared to that of the ionized parent copolymer (IBMA‐Na, Mw ∼350 kg/mol), suggesting intramolecular aggregation of the alkyl side‐chain groups along the polymer backbone. The copolymer modified with the longer chain n‐decyl, on the other hand, forms stable large intermolecular aggregates containing 33 chains/aggregate. The copolymers of maleic acid–sodium salt and styrene (SMA‐Na) appear to have no signs of aggregation, despite being a hydrophobic polyelectrolyte. The copolymer of maleic acid–sodium salt and di‐isobutylene (DIBMA‐Na) has a similar salting‐out concentration as SMA‐Na. The radius of gyration measurements by static light scattering suggest that at least some fraction of the DIBMA‐Na chains form large intermolecular aggregates. The copolymers of maleic acid–sodium salt with n‐alkenes (n‐CmMA‐Na) in 0.1 N NaAc form small intermolecular aggregates (three to five chains/aggregate). In contrast to these static light scattering results, PGSE NMR diffusion measurements for the above aggregated systems indicate only one diffusion coefficient consistent with the motion of single isolated chains. A plausible explanation for this discrepancy is that the population of the aggregates is too small to be sufficiently detected in the PGSE NMR experiment. Furthermore, it is likely that the aggregate has a larger relaxation rate than the nonaggregate, and therefore has a comparatively reduced signal in the PGSE NMR experiment. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 3584–3597, 2004
The behavioural response of slugs and snails to novel molluscicides, irritants and repellents
Authors: Schüder Ingo , Port Gordon , Bennison Jude
Published: August 2004

The behavioural response of the slug Deroceras panormitanum (Lessona and Pollonera) and the snail Oxyloma pfeifferi (Rossmässler) to novel molluscicides was investigated in choice and no‐choice experiments. Low‐light video‐recording in combination with automated tracking and event recording was used to identify the repellent and irritant effects of (1) cinnamamide, (2) copper ammonium carbonate, (3) a mulch, (4) a horticultural ground‐cover matting impregnated with a copper formulation and (5) urea/formaldehyde. In the no‐choice experiments the products had a stronger irritant effect on the snails than on the slugs. All products tested except the mulch significantly reduced the locomotor activity of both the slugs and snails. The most effective product, cinnamamide, reduced snail locomotor activity by 94% and track length by 96%. The overall repellent effect of the treatments in the choice experiments was stronger in the slugs; where presence, locomotor activity and track length in the treated area were significantly reduced by all products. The avoidance of treated areas exceeded 95% with the mulch (for slugs) and with copper ammonium carbonate (for snails). Copyright © 2004 Society of Chemical Industry
Carotenoid‐induced quenching of the phycobilisome fluorescence in photosystem II‐deficient mutant of Synechocystis sp.
Authors: Rakhimberdieva Marina G. , Stadnichuk Igor N. , Elanskaya Irina V. , Karapetyan Navassard V.
Published: August 2004

Brief – 10‐second long – irradiation of a photosystem II‐deficient mutant of cyanobacterium Synechocystis sp. PCC 6803 with intense blue or UV‐B light causes an about 40% decrease of phycobilisome (PBS) fluorescence, slowly reversible in the dark. The registered action spectrum of PBS fluorescence quenching only shows bands at 500, 470 and 430 nm, typical of carotenoids, and an additional UV‐B band; no peaks in the region of chlorophyll or PBS absorption have been found. We propose that quenching induced by carotenoids, possibly protein‐bound or glycoside, reveals a new regulatory mechanism protecting photosynthetic apparatus of cyanobacteria against photodamage.
Zur Dimensionalität und Konstruktvalidität eines videobasierten, objektiven Persönlichkeitstests
Authors: Hergovich Andreas , Arendasy Martin E. , Sommer Markus , Bognar Bettina , Olbrich Andreas
Published: August 2004

Zusammenfassung: Die vorliegende Studie berichtet über erste Ergebnisse zur Dimensionalität und Konstruktvalidität eines neu entwickelten, videobasierten, objektiven Persönlichkeitstests zur Erfassung der Risikobereitschaft in Verkehrssituationen. Ausgehend vom Modell der Risikohomöostase nach Wilde (1978 , 1994 ) wurden unterschiedliche Verkehrsszenen gefilmt, wobei der Grad an objektiver Gefährdung über die einzelnen Situationen hinweg variiert. Die Personen haben die Aufgabe anzugeben, ab welchem Zeitpunkt die Ausführung der beschriebenen situationskontingenten Handlung ihrer Meinung nach zu gefährlich sei. Als Maß für den subjektiv akzeptierten Risikograd einer Person im Sinne der Risikohomöostase-Theorie von Wilde (1978 , 1994 ) wurden itemweise Latenzzeiten erhoben. In einer Studie mit insgesamt 243 Personen konnte die Eindimensionalität des Verfahrens im Sinne des Latency-Modells von Scheiblechner (1978 , 1979 , 1985 ) nachgewiesen werden. Erste Hinweise zur Konstruktvalidität des Verfahrens werden gegeben.
Motivinhalte und Handlungs- versus Lageorientierung
Authors: Olvermann Ramona , Metz-Göckel Hellmuth , Hannover Bettina , Pöhlmann Claudia
Published: August 2004

Zusammenfassung: Personen unterscheiden sich darin, wie stark sie ihr Selbst als autonom und unabhängig vom sozialen Kontext (Independente) oder aber als sozial und verbunden mit dem Kontext (Interdependente) definieren. Während die Auswirkungen der Selbstkonstruktion auf kognitive Variablen Gegenstand zahlreicher Studien gewesen sind, wurden mögliche Beziehungen zu motivationalen Prozessen bisher kaum geprüft. Es werden drei Studien vorgestellt, in denen Zusammenhänge zwischen Personunterschieden in motivationalen/volitionalen Tendenzen und interindividuellen Unterschieden in der Art der Selbstkonstruktion untersucht wurden. Unsere Annahme war, dass sich Independente von Interdependenten sowohl in den Inhalten unterscheiden, die in ihren Motiven dominieren, als auch darin, auf welche Art und Weise sie Handlungsabsichten in die Tat umsetzen. Erwartungsgemäß waren Interdependente stärker anschlussmotiviert und weniger leistungsmotiviert, und sie zeigten sich stärker durch Furcht vor Misserfolg motiviert als Independente (Studien 2 und 3, Inhalte). Weiter Interdependente stärker lageorientiert und weniger handlungsorientiert als Independente (Studie 1, Art der Umsetzung von Absichten in Handlungen).
Sensitivity studies of cirrus clouds formed by heterogeneous freezing in the ECHAM GCM
Authors: Lohmann U. , Kärcher B. , Hendricks J.
Published: August 2004

Cirrus clouds can form by homogeneous and heterogeneous ice nucleation mechanisms at temperatures below 235 K. Here we evaluate the effectiveness of heterogeneous freezing versus homogeneous freezing using a newly developed parameterization of heterogeneous freezing that is restricted to immersion freezing as the most likely pathway for heterogeneous ice formation in cirrus conditions [Kärcher and Lohmann, 2003]. In addition to a reference simulation considering homogeneous nucleation with temperature‐dependent freezing thresholds, we discuss two idealized model experiments. We conduct a scenario that hypothetically assumes that the aerosol particles available for homogeneous freezing could act as freezing nuclei commencing freezing at 130% with respect to ice and contrast that by a scenario that only considers black carbon and mineral dust as immersion nuclei with the same freezing relative humidity of 130%. These idealized simulations serve to delimit possible climate responses. If the number of freezing nuclei is limited by the number of black carbon and dust aerosols, then heterogeneous freezing results in fewer ice crystals than formed by homogeneous freezing. These fewer ice crystals grow more readily to precipitation size and with that increase the global mean precipitation, decrease the ice water path, and trap less outgoing longwave radiation at the top of the atmosphere.
Analysis of wave fields by Fourier integral operators and their application for radio occultations
Authors: Gorbunov M. E. , Lauritsen K. B.
Published: August 2004

Fourier integral operators (FIOs) are used for constructing asymptotic solutions of wave problems and for the generalization of the geometrical optics. Geometric optical rays are described by the canonical Hamilton system, which can be written in different canonical coordinates in the phase space. The theory of FIOs generalizes the formalism of canonical transforms for solving wave problems. The FIO associated with a canonical transform maps the wave field to a different representation. Mapping to the representation of ray impact parameter was used in the formulation of the canonical transform (CT) method for processing radio occultation data. The full‐spectrum inversion (FSI) method can also be looked at as an FIO associated with a canonical transform of a different type. We discuss the general principles of the theory of FIOs and formulate a generalization of the CT and FSI techniques. We derive the FIO that maps radio occultation data measured along the low Earth orbiter orbit without first applying back propagation. This operator is used for the retrieval of refraction angles and atmospheric absorption. We give a closed derivation of the exact phase function of the FIO obtained in the “phase matching” approach by Jensen et al. [2004] We derive a novel FIO algorithm denoted CT2, which is a modification and improvement of FSI. We discuss the use of FIOs for asymptotic direct modeling of radio occultation data. This direct model is numerically much faster then the multiple phase screen technique. This is especially useful for simulating LEO‐LEO occultations at frequencies of 10–30 GHz.
Influence of ocean‐atmosphere coupling on the properties of tropical instability waves
Authors: Pezzi Luciano P. , Vialard Jérôme , Richards Kelvin J. , Menkes Christophe , Anderson David
Published: August 2004

In this study we investigate how the modulation of surface wind‐stress by tropical instability waves (TIWs) feeds back onto TIWs and plays a role in their fundamental properties. An ocean general circulation model is used, that reproduces qualitatively well the properties of TIWs when forced by climatological winds, although with a 30% underestimated amplitude. The ocean model is coupled to the atmosphere through a simple parameterization of the wind stress response to SST. The properties of the TIWs in the coupled simulations are compared with those without active coupling. Active coupling results in a negative feedback on TIWs, slightly reducing their temperature and meridional current variability, both at the surface and sub‐surface. This reduced activity modulates the meridional heat and momentum transport, resulting in modest changes to the mean state, with a cooler cold tongue and stronger equatorial currents.
Significance of the vertical profile of the Indonesian Throughflow transport to the Indian Ocean
Authors: Song Qian , Gordon Arnold L.
Published: August 2004

Using an ocean general circulation model, we find that the vertical profile of the Indonesian Throughflow (ITF) transport is important in regulating the stratification and surface heat fluxes of the Indian Ocean. With the same total ITF transport, a thermocline‐intensified ITF, relative to a surface‐intensified ITF, not only cools the surface layer of the Indian Ocean while warming the Indian Ocean below the thermocline, but also induces negative temperature anomalies at the sea surface throughout the Indian basin. As a consequence of this surface effect the net heat gain of the Indian Ocean is increased. The results suggest that it is necessary to properly represent the vertical profile of ITF transport within ocean and climate numerical models.