bluuebunny/crossref_metadata_2025 huggingface dataset:
Industrial ecology, life cycles, supply chains: differences and interrelations
Authors: Seuring Stefan
Published: August 2004

Within recent years, various concepts have arisen in environmental management that directly address the flow of material (and information) along life cycles or supply chains and thereby relate to inter‐organizational management aspects. These include industrial ecology (IE), life‐cycle management, closed‐loop supply chains, integrated chain management and green/environmental or sustainable supply chain management. It is not clear how these concepts relate to each other and whether or how they are different. Starting with sustainable development three criteria are identified that allow the comparison of the four concepts. Building on definitions the concepts are discussed and analysed using the three criteria while also identifying a distinctive feature of each approach. The criteria reveal that the concepts take a specific approach to study material flows in their particular system boundaries. This also relates to the time frame usually applied within the concept as well as the relevant actor network taken into account. Beyond these differences, it arises that the concepts have their strengths on different levels, which leads to a framework for the interrelation of the concepts. Copyright © 2004 John Wiley & Sons, Ltd and ERP Environment.
Networking for knowledge transfer: towards an understanding of local authority roles in regional industrial ecosystem management
Authors: von Malmborg Fredrik
Published: August 2004

Knowledge of the changing roles of local authorities (LAs) in relation to industry would provide an important insight for development and management of industrial ecology at the regional level. Drawing on empirical studies in Sweden, this paper develops a theoretical understanding of the roles of LAs in knowledge transfer in regional environmental management networks. It is suggested that LAs, besides initiating networks and being network brokers and managers, can act as ‘knowledge banks’ or ‘knowledge brokers’. As a ‘knowledge bank’, officers in the LA hold the knowledge transferred to companies and engage closely with the companies in small active networks. As ‘knowledge brokers’, LA officers are less active and mainly help companies to get in contact with consultants and technical experts who hold the knowledge needed for developing environmental management in the companies. In all, the roles identified could be seen as more specific approaches to be taken by the LA when playing the overall role of an institutional anchor tenant, facilitating development and management of regional industrial ecosystems. Copyright © 2004 John Wiley & Sons, Ltd and ERP Environment.
Estimation of low concentrations in the presence of high concentrations using Bayesian algorithms for interpretation of spectrophotometric data
Authors: Niedziński Cezary , Morawski Roman Z.
Published: August 2004

A Bayesian method for interpretation of spectral data, dedicated to the monitoring‐type applications of mini‐ and micro‐spectrometers, is addressed. The method generates estimates of the concentrations of the components of an analyzed substance on the basis of the data representative of its absorption spectrum, provided that both the normalized spectra of the components and statistical information on historical measurements of the monitored concentrations are available. The Bayesian method is systematically compared with the constrained least‐squares method, under an assumption that the estimated concentrations differ considerably and the processed data are subject not only to random instrumental noise but also to some random disturbances introduced by the residual content of components of the analyzed substance being not identified. A study, performed using both synthetic and real‐world spectrophotometric data, is aimed at the assessment of the robustness of the Bayesian method to the maximum‐to‐minimum ratio of concentrations and imprecision ofa prioriinformation. Copyright © 2004 John Wiley & Sons, Ltd.
Three‐way component analysis of interval‐valued data
Authors: Giordani Paolo , Kiers Henk A. L.
Published: August 2004

Vertices Principal Component Analysis (V‐PCA) and Centers Principal Component Analysis (C‐PCA) are variants of Principal Component Analysis (PCA) to deal with two‐way interval‐valued data. In this case the observation units are represented as hyperrectangles instead of points. Tucker3 and CANDECOMP/PARAFAC are component analysis techniques to analyze the underlying structure of three‐way data sets. In the present paper, after recalling the above mentioned methods, we extend the C‐PCA and V‐PCA methods to deal with three‐way interval‐valued data by means of Tucker3 and CANDECOMP/PARAFAC and we describe how to represent the observation units in the obtained low‐dimensional space. Furthermore, an application of the extended methods—called Three‐way Vertices Principal Component Analysis (3V‐PCA) and Three‐way Centers Principal Component Analysis (3C‐PCA)—to three‐way interval‐valued air pollution data is described. Copyright © 2004 John Wiley & Sons, Ltd.
Mesostructured Silica Tubes and Rods by Templating Porous Membranes
Authors: Liang Zhijian , Susha Andrei S.
Published: August 2004

Mesostructured silica tubes and rods were prepared by deposition of a prehydrolysed silica sol with surfactant onto the cylindrical pores of a polycarbonate (PC) membrane template, followed by calcination to remove the surfactant and membrane template. The tubular and rodlike morphologies of mesostructured silica were demonstrated by scanning electron microscopy (SEM) and transmission electron microscopy (TEM) measurements. The tubes and rods show ordered hexagonal mesostructures, which were demonstrated by small angle X‐ray diffraction (XRD) patterns and TEM measurements.
Numerical modelling of elastomers using the boundary element method
Authors: Bayliss M. T. , El‐Zafrany A.
Published: August 2004

The FEM analysis of hyper elastic, elastomeric materials has been formulated and implemented for various material models (strain energy functions) over the years. More recently, the analysis of elastomeric materials has been attempted in the boundary element method. This has been achieved by the addition of non‐linear domain terms to the basic linear boundary element equation. These non‐linear domain terms require the evaluation of the displacement derivative components directly from displacement derivative boundary integral equations. In the solution to the boundary problem it is required to regularize the different types of singularities occurring in the system of non‐linear boundary integral equations. This paper discusses the necessary theory for the boundary element method as applied to elastomers and presents a comparison between semi‐analytical and numerical solutions for various test cases. Copyright © 2004 John Wiley & Sons, Ltd.
CD3 bright lymphocyte population reveal γδ T cells
Authors: Lambert Claude , Genin Christian
Published: August 2004

Background

In routine CD3/CD4/CD8 T‐cell analysis, a CD3 bright population of lymphocytes is frequently observed. The aim of the present study was to identify the immunological significance of such CD3 bright lymphocytes.

Methods

We analyzed samples from 31 healthy adult volunteers, 78 human immunodeficiency virus (HIV)‐positive, and 78 renal transplanted patients.

Results

A clearly distinct CD3 bright (frequently CD4−/CD8−) T‐cell fraction was observed in 84% of donors and was directly correlated with the fraction of γδ T cells (r2 = 0.64). CD3 overexpression on γδ T cells was confirmed by a combination of monoclonal antibody staining (CD3‐ECD, γδTCR‐FITC, and αβTCR‐PE‐Cy5) or immunomagnetic purification of γδ T cells (i.e., MdFI 20 vs 8.86). The γδ T cells expressed CD8 polypeptide chains (α and β) in all possible combinations. The largest proportion, surprisingly, were cells expressing CD8ββ homodimers (43.8 ± 16.5%). CD8αα homodimers were expressed on 14.2% (± 12.3) of total γδ T cells, whereas CD8αβ heterodimers were expressed on 12.2% (± 7.5). We also observed a bimodal distribution of the intensity of CD3 fluorescence of γδ T cells in immunocompromised patients with a threshold at 105 cell/μl. CD3 bright γδ T cells were more frequently observed in HIV patients (29%) compared with renal transplant patients (11%) and healthy donors (3%; χ 2 test: P = 0.0007).

Conclusions

The simple observation of a CD3 bright T‐cell subset on CD3/CD4/CD8 routine analysis suggests a high γδ T‐cell fraction and, in our opinion, should be followed by a complementary analysis to determine precisely the number of γδ T cells and to identify their CD8α/β phenotype. When CD3 bright T cells/μl were more than 40%, high γδ T cells were detected in more than 87% of cases, with a specificity of 76%. Occasionally, the CD3 bright subset appeared to be strongly homogeneous, suggesting an oligoclonal proliferation that could possibly reveal a chronic localized stimulation or an early lymphoproliferative disorder. Because the γδ T cells have interesting immunological peculiarities, the clinical significance of their quantitative abnormality should be clarified in diseases such as HIV, organ transplantation, autoimmunity and lymphoma. © 2004 Wiley‐Liss, Inc.
Heat shock protein 60 from Chlamydia pneumoniae elicits an unusual set of inflammatory responses via Toll‐like receptor 2 and 4 in vivo
Authors: da Costa Clarissa U. Prazeres , Wantia Nina , Kirschning Carsten J. , Busch Dirk H. , Rodriguez Nuria , Wagner Hermann , Miethke Thomas
Published: August 2004

Heat shock protein 60 (HSP60) from Chlamydia pneumoniae was described to trigger in vitro inflammatory and cytokine responses including TNF and IL‐12p40. Although it can be found in atherosclerotic plaques of patients, the stimulatory potential of chlamydial and other HSP60 in vivo is unclear. We now report that chlamydial HSP60 fails to induce TNF expression in vivo, and significant serum levels of IL‐12p40 are only found upon intraperitoneal injection of high doses of HSP60 or after intravenous application. Upon purification of chlamydial HSP60 with polymyxin B‐agarose columns, its ability to induce TNF secretion in vitro is much reduced. However, purified chlamydial HSP60 causes increased serum levels of the CXC chemokines KC and MIP2 in vivo, as well as a strong accumulation of polymorphonuclear neutrophils (PMN) in the peritoneal cavity upon intraperitoneal challenge. With respect to PMN accumulation, chlamydial HSP60 is more potent than endotoxin or the CpG oligonucleotide 1668. The responses observed are completely abolished in Toll‐like receptor (TLR)2/4‐double‐deficient mice, while single‐deficient mice respond almost normally. Furthermore, KC induction and PMN accumulation are largely dependent on MyD88. In conclusion, HSP60 from C. pneumoniae triggers inflammatory responses in vivo that differ from responses induced by endotoxin or CpG oligonucleotides and are dependent on TLR2 and 4.
Transcriptional activation induced in macrophages by Toll‐like receptor (TLR) ligands: from expression profiling to a model of TLR signaling
Authors: Schmitz Frank , Mages Jörg , Heit Antje , Lang Roland , Wagner Hermann
Published: August 2004

Toll‐like receptors (TLR) sense microbial compounds and bridge innate and adaptive immunity by activation of antigen‐presenting cells. TLR‐induced signaling via intracellular adaptor molecules, including MyD88 and TRIF, drives transcriptional activation of genes including pro‐inflammatory cytokines and cell activation markers. To globally assess the activation programs triggered by individual TLR in macrophages, we used microarray‐based gene expression profiling of the murine macrophage cell line RAW264.7. Here we describe that the TLR4 ligand LPS more strongly modulates gene expression compared to ligands for TLR 2, 3, 7, and 9. Taking advantage of the known dependency of TLR on given adaptor molecules, we operationally define sets of MyD88 and TRIF “private” genes. We conclude with a TLR signaling model that incorporates both negative and synergistic interactions of MyD88‐ and TRIF‐controlled signaling pathways as deduced from the microarray data presented.
Interleukin‐6 is a direct mediator of T cell migration
Authors: Weissenbach Manuela , Clahsen Thomas , Weber Christian , Spitzer Dirk , Wirth Dagmar , Vestweber Dietmar , Heinrich Peter C. , Schaper Fred
Published: August 2004

Interleukin (IL)‐6 is a pleiotropic cytokine involved in the differentiation and proliferation of hematopoietic cells. Hepatocytes respond to IL‐6 with the synthesis and secretion of acute‐phase proteins. In addition, IL‐6 plays a role as a migration factor in vivo. In the present paper, we studied the potential of IL‐6 to mediate migration of human primary T cells and T cell‐derived cell lines. IL‐6 was found to induce migration only in the presence of extracellular matrix, suggesting a cross‐talk between the IL‐6‐ and integrin signal transduction pathways. Furthermore, an IL‐6 gradient is required for chemotactic migration. This activity is not due to the release of secondary chemotactic activities, but is a direct response to IL‐6. T cell migration could also be observed in response to IL‐11, but no migration was found after stimulation with leukemia inhibitory factor or oncostatin M, although these cytokines signal through gp130‐containing receptor complexes. Finally, we present evidence that activation of the mitogen‐activated protein kinase (MAPK) cascade, the phosphatidylinositol 3‐kinase as well as the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway is crucial for IL‐6‐induced migration. Selective activation of the JAK/STAT or the MAPK cascade by mutated receptor proteins shows a crucial role of IL‐6‐initiated SH2 domain‐containing tyrosine phosphatase 2/MAPK activity for migration.
Commentary: Keeping track of pro‐B cells: a new model for the effects of IL‐7 during B cell development
Authors: Monroe John G. , Allman David
Published: August 2004

Trophic and instructive models have been invoked to explain how various cytokines influence the survival, proliferation and differentiation of lymphoid progenitors. There is evidence that IL‐7 can act in either a trophic or an instructive manner during B and T cell development although its roles in B cell development in the fetus versus the adult mouse and in the mouse versus the human may vary. Here we outline the stages of B cell development and the conventional model of the role of IL‐7 in the transitions from pro‐B cells to pre‐B cells and then to immature B cells. We also discuss the implications of recent data that have led to a new model for this process.

See accompanying article: http://dx.doi.org/10.1002/eji.200425400
The spread of a viral infection in a plantation
Authors: Gani J. , Stals L.
Published: August 2004

We consider a plantation subject to viral infection, in which infected plants are replaced by plants from a nursery, also subject to a minor degree of infection. A discrete time Markov chain model for the spread of infection in the plantation is proposed, and its consequences derived. The expected number of healthy plants in the plantation is obtained in the stationary case, and some conclusions drawn about the effect of the level of infection in the nursery on that in the plantation. Copyright © 2004 John Wiley & Sons, Ltd.
A robust statistical procedure for evaluating genotoxicity data
Authors: Hothorn Ludwig A.
Published: August 2004

The statistical evaluation of in vitro genotoxicity data is commonly performed by dose–response analysis. Common trend tests cannot be recommended because non‐monotonicity may occur due to the use of high dose levels. Several decision tree approaches using preliminary comparisons versus control and conditional eliminating of high doses were proposed. Their heuristic and conservative behavior can be overcome by multiple contrast test, which test on trend and on comparisons versus control simultaneously. Other versions of protected trend test were investigated—each sensitive to any shape of the dose–response. A simple bootstrap approach is proposed using SAS PROC MULTTEST for the analysis of real genotoxicity data. Copyright © 2004 John Wiley & Sons, Ltd.
Geochronological evidence for pervasive Miocene weathering, Minas Gerais, Brazil
Authors: Carmo Isabela de O. , Vasconcelos Paulo
Published: August 2004

40Ar/39Ar laser incremental‐heating analyses of 22 individual grains of supergene cryptomelane from three weathering proﬁles, up to 400 km apart, in the Rio Doce valley and Barbacena regions at Minas Gerais, Brazil, show that the formation of weathering proﬁles in these regions is contemporaneous, suggesting a strong weathering event in the Middle to Late Miocene (10–8 Ma). The preservation of these Miocene samples at or near the present surface suggests that either erosion rates have been very low in the region since the Miocene or that a much thicker weathering mantle was present in the region originally. Assuming a constant thickness of weathering proﬁles in the region throughout the Tertiary, we may calculate weathering front propagation rates of 4–8 m Myr−1 during the past 10 Ma. Copyright © 2004 John Wiley & Sons, Ltd.
A patch hierarchy approach to modeling surface and subsurface hydrology in complex flood‐plain environments
Authors: Poole G. C. , Stanford J. A. , Running S. W. , Frissell C. A. , Woessner W. W. , Ellis B. K.
Published: August 2004

Geomorphology interacts with surface‐ and ground‐water hydrology across multiple spatial scales. Nonetheless, hydrologic and hydrogeologic models are most commonly implemented at a single spatial scale. Using an existing hydrogeologic computer model, we implemented a simple hierarchical approach to modeling surface‐ and ground‐water hydrology in a complex geomorphic setting. We parameterized the model to simulate ground‐ and surface‐water ﬂow patterns through a hierarchical, three‐dimensional, quantitative representation of an anabranched montane alluvial ﬂood plain (the Nyack Flood Plain, Middle Fork Flathead River, Montana, USA). Comparison of model results to ﬁeld data showed that the model provided reasonable representations of spatial patterns of aquifer recharge and discharge, temporal patterns of ﬂood‐water storage on the ﬂood plain, and rates of ground‐water movement from the main river channel into a large lateral spring channel on the ﬂood plain, and water table elevation in the alluvial aquifer. These results suggest that a hierarchical approach to modeling ground‐ and surface‐water hydrology can reproduce realistic patterns of surface‐ and ground‐water ﬂux on alluvial ﬂood plains, and therefore should provide an excellent ‘quantitative laboratory’ for studying complex interactions between geomorphology and hydrology at and across multiple spatial scales. Copyright © 2004 John Wiley & Sons, Ltd.
Analysis of landslide frequencies and characteristics in a natural system, coastal British Columbia
Authors: Guthrie R. H. , Evans S. G.
Published: August 2004

Two hundred and one debris slides and debris ﬂows were analyzed in a 286 km2 study area on the west coast of Vancouver Island, British Columbia, Canada. The study area remains essentially untouched by humans and therefore affords a natural setting in which to examine slope processes. Landslides were identiﬁed and characterized on aerial photographs from 1:15 000 to 1:31 680, and were then mapped and transferred to a GIS for analysis. Based on detailed landslide surveys, we propose a new method to accurately determine volume of landslides of this type by measured total area. Results indicate average denudation rates of 56 m3 y−1 km−2, and higher natural rates of failure than analogous regions in coastal British Columbia. In contrast, the landslide rates are substantially less than those from forested watersheds. Landslide distribution is spatially clustered in air photograph epochs, and we propose intense storm cells within regional events as the causal mechanism. Further, failures occurred preferentially over the West Coast Crystalline Complex (by 1·4 times), a metamorphic assemblage of gabbros, schists and amphibolites, but 1·5 times less often over the Island Plutonic Suite, a granitic intrusive formation. The former result represents a new ﬁnding, while the latter corroborates ﬁndings of previous authors. We examined magnitude–frequency relationships of the data set and present for the ﬁrst time a strong argument that the rollover effect is not merely an artefact, but is instead a consequence of the physical characteristics of the landslides themselves. We subsequently analyzed magnitude–frequency relationships from two other complete data sets from coastal British Columbia and produced a family of curves corroborating this result. Copyright © 2004 John Wiley & Sons, Ltd.
Attracting and maintaining infant attention during habituation: Further evidence of the importance of stimulus complexity
Authors: Richard Jacques F. , Normandeau Joane , Brun Véronique , Maillet Mario
Published: August 2004

We examined the effect of stimulus complexity and frequency on infants' attention responses during an auditory habituation procedure. Five stimuli of different complexity and frequency were presented repeatedly to 80 5‐month‐old infants. Quicker attention‐getting and longer attention‐holding responses were obtained with the more complex stimuli. Furthermore, a progressive decrease in attention‐holding, but not in attention‐getting, was observed across trials. The findings are similar to those well established in the visual modality [e.g., Cohen et al. (Child Dev. 1975; 46: 611); Slater et al. (Br. J. Dev. Psychol. 1984; 2: 287)] showing that auditory complexity is an important variable in attracting and maintaining infant attention, and that only attention‐holding is subject to habituation. Although the complex stimulus contained higher frequencies than the simple or intermediate stimuli, our results further showed that stimulus frequency alone had no significant effect on attention‐getting or attention‐holding, which strengthens our claim that complexity preference during habituation can be generalized to the auditory modality. Copyright © 2004 John Wiley & Sons, Ltd.
Hierarchy of interactive functions in father‐mother‐baby three‐way games
Authors: Frascarolo France , Favez Nicolas , Carneiro Claudio , Fivaz‐Depeursinge Elisabeth
Published: August 2004

In developmental research, the family has mainly been studied through dyadic interaction. Three‐way interactions have received less attention, partly because of their complexity. This difficulty may be overcome by distinguishing between four hierarchically embedded functions in three‐way interactions: (1) participation (inclusion of all participants), (2) organization (partners keeping to their roles), (3) focalization (sharing a common focus) and (4) affective contact (being in tune). We document this hierarchical model on a sample of 80 families observed in the Lausanne Trilogue Play situation across four different sites. Hierarchy between functions was demonstrated by means of Guttman scalability coefficient. Given the importance of the child's development in a threesome, the pertinence of this model for family assessment is discussed. Copyright © 2004 John Wiley & Sons, Ltd.
Sodium 4‐phenylbutyrate induces apoptosis of human lung carcinoma cells through activating JNK pathway
Authors: Zhang Xing , Wei Lin , Yang Yu , Yu Qiang
Published: August 2004

Sodium 4‐phenylbutyrate (PB) has been used in the therapy of urea cycle defects for many years. Recently, it has been shown to cause cellular differentiation, growth arrest, and apoptosis in certain malignancies. We have analyzed the effects of PB on human lung carcinoma cells. PB has distinct patterns of effects on different lung carcinoma cells, inducing apoptosis in NCI‐H460 and NCI‐H1792 cells, causing G1 arrest in A549 and SK‐LU‐1 cells, but having no effect on a non‐transformed bronchial epithelial cell line HBE4‐E6/E7. We investigated the role of MAP kinase family members, extracellular signal‐regulated kinase (ERK), JNK, and p38 mitogen‐activated protein kinase (MAPK), as well as other important cell survival signaling molecules in PB‐induced apoptosis. We observed activation of JNK and ERK by PB in the lung cancer cells. JNK was activated only in the two apoptotic cells, whereas ERK was activated in both the apoptotic and the growth‐arrested cells, demonstrating a correlation between apoptosis and activation of JNK in response to PB. Both JNK inhibitor and JNK RNA interference (RNAi) inhibited PB‐induced apoptosis, whereas MEK inhibitor did not, supporting that apoptosis induced by PB is through activation of JNK. De novo protein synthesis is required for the PB‐induced JNK activation and induction of apoptosis. However, the production of known upstream activators of JNK, namely Fas/Fas ligand, tumor necrosis factor (TNF)‐α, TNF‐β, and TRAIL, are not altered by PB treatment. Therefore, PB activates JNK through an unidentified and cell type‐specific mechanism. Understanding of this mechanism is of therapeutic value in treating cancer patients with PB. © 2004 Wiley‐Liss, Inc.
Regulation of RANKL promoter activity is associated with histone remodeling in murine bone stromal cells
Authors: Fan Xian , Roy Eileen M. , Murphy Tamara C. , Nanes Mark S. , Kim Sungtae , Pike J. Wesley , Rubin Janet
Published: August 2004

Receptor activator of NFκ‐B ligand (RANKL) is essential for osteoclast formation, function, and survival. Although RANKL mRNA and protein levels are modulated by 1,25(OH)2D3 and other osteoactive factors, regulatory mechanisms remain unclear. In this study, we show that 2 kb or 2 kb plus exon 1 of a RANKL promoter sequence conferred neither 1,25(OH)2D3 response nor tissue specificity. The histone deacetylase inhibitors trichostatin A (TSA) and sodium butyrate (SB), however, strongly increased RANKL promoter activity. A series of 5′‐deleted RANKL promoter constructs from 2,020 to 110 bp showed fourfold increased activity after TSA treatment. TSA also dose dependently enhanced endogenous RANKL mRNA expression with 50 μM of TSA treatment causing equivalent RANKL expression to that seen with 1 nM 1,25(OH)2D3. Using a chromatin immunoprecipitation (ChIP) assay we showed that TSA significantly enhanced association of both acetylated histone H3 and H4 on the RANKL promoter, with H4 > H3. A similar increase in acetylated histone H4 on the RANKL gene locus was seen after 1,25(OH)2D3 treatment, but ChIP assay did not reveal localization of VDR/RXR heterodimers on the putative VDRE of the RANKL promoter. To explore the role of H4 acetylation of 1,25(OH)2D3 stimulated RANKL, we added both TSA and 1,25(OH)2D3 together. While the combination further increased acetylation of H4 on the RANKL locus, surprisingly, TSA inhibited 1,25(OH)2D3‐induced RANKL mRNA expression by 70% at all doses of 1,25(OH)2D3 studied. These results suggest that TSA increases of endogenous expression of RANKL involve enhanced acetylation of histones on the proximal RANKL promoter. Preventing deacetylation, however, blocks 1,25(OH)2D3 action on this gene. Chromatin remodeling is therefore involved in RANKL expression. © 2004 Wiley‐Liss, Inc.
Cluster computing for digital microscopy
Authors: Carrington Walter A. , Lisin Dimitri
Published: August 2004

Microscopy is becoming increasingly digital and dependent on computation. Some of the computational tasks in microscopy are computationally intense, such as image restoration (deconvolution), some optical calculations, image segmentation, and image analysis. Several modern microscope technologies enable the acquisition of very large data sets. 3D imaging of live cells over time, multispectral imaging, very large tiled 3D images of thick samples, or images from high throughput biology all can produce extremely large images. These large data sets place a very large burden on laboratory computer resources. This combination of computationally intensive tasks and larger data sizes can easily exceed the capability of single personal computers. The large multiprocessor computers that are the traditional technology for larger tasks are too expensive for most laboratories. An alternative approach is to use a number of inexpensive personal computers as a cluster; that is, use multiple networked computers programmed to run the problem in parallel on all the computers in the cluster. By the use of relatively inexpensive over‐the‐counter hardware and open source software, this approach can be much more cost effective for many tasks. We discuss the different computer architectures available, and their advantages and disadvantages. Microsc. Res. Tech. 64:204–213, 2004. © 2004 Wiley‐Liss, Inc.
Colocalization analysis yields superior results after image restoration
Authors: Landmann Lukas , Marbet Permsin
Published: August 2004

Colocalization analysis is a powerful tool for the demonstration of spatial and temporal overlap in the distribution patterns of fluorescent probes. In unprocessed images, background affects image quality by impairing resolution and obscuring image detail in the low‐intensity range. Because confocal images suffer from background levels up to 30% maximum intensity, colocalization analysis, which is a typical segmentation process, is limited to high‐intensity signal. In addition, noise‐induced, false‐positive events (“dust”) may skew the results. Therefore, suppression of background is crucial for this type of image analysis. Analysis of synthetic and biological objects demonstrates that median filtering is able to eliminate noise‐induced colocalization events successfully. Its disadvantages include the occasional generation of false‐positive and false‐negative results as well as the inherent impairment of resolution. In contrast, image restoration by deconvolution suppresses background to very low levels (<10% maximum intensity), which makes additional objects in the low‐intensity but high‐frequency range available for analysis. The improved resolution makes this technique extremely suitable for examination of objects of near resolution size as demonstrated by correlation coefficients. Deconvolution is, however, sensitive to overestimation of the background level. Conclusions for practical application are: (1) In raw images, colocalization analysis is limited to the intensity range above the background level. This means the higher the RS/N the better. Unfortunately, images of most biological specimens have a low RS/N. (2) Filtering improves the result substantially. The reduction of background levels and the concomitant increase of the RS/N are generated at the expense of resolution. This is a quick and simple method in cases where resolution is not a major concern. (3) If colocalization in the low‐intensity range and/or maximum resolution play a role, deconvolution should be used. Microsc. Res. Tech. 64:103–112, 2004. © 2004 Wiley‐Liss, Inc.
AFM/CLSM data visualization and comparison using an open‐source toolkit
Authors: Rajwa Bartek , Mcnally Helen A. , Varadharajan Padma , Sturgis Jennifer , Robinson J. Paul
Published: August 2004

There is a vast difference in the traditional presentation of AFM data and confocal data. AFM data are presented as surface contours while confocal data are usually visualized using either surface‐ or volume‐rendering techniques. Finding a common meaningful visualization platform is not an easy task. AFM and CLSM technologies are complementary and are more frequently being used to image common biological systems. In order to provide a presentation method that would assist us in evaluating cellular morphology, we propose a simple visualization strategy that is comparative, intuitive, and operates within an open‐source environment of ImageJ, SurfaceJ, and VolumeJ applications. In order to find some common ground for AFM‐CLSM image comparison, we have developed a plug‐in for ImageJ, which allows us to import proprietary image data sets into this application. We propose to represent both AFM and CLSM image data sets as shaded elevation maps with color‐coded height. This simple technique utilizes the open source VolumeJ and SurfaceJ plug‐ins. To provide an example of this visualization technique, we evaluated the three‐dimensional architecture of living chick dorsal root ganglia and sympathetic ganglia measured independently with AFM and CLSM. Microsc. Res. Tech. 64:176–184, 2004. © 2004 Wiley‐Liss, Inc.
Automated acquisition and processing of multidimensional image data in confocal in vivo microscopy
Authors: Kozubek Michal , Matula Petr , Matula Pavel , Kozubek Stanislav
Published: August 2004

The successful development of visualization techniques for live cell imaging leads to the development of suitable software for the acquisition and processing of multidimensional image data. This report compares several possible approaches to image acquisition and processing in confocal in vivo microscopy and suggests new alternatives to the published methods. Special attention is paid to spinning disk systems based either on a classical Nipkow disk or on the microlens principle. This study shows how to optimize image acquisition process in live cell studies using camera binning feature and how to perform object tracking using a new fast image registration method based on the graph theory. Microsc. Res. Tech. 64:164–175, 2004. © 2004 Wiley‐Liss, Inc.
Alignment of the cell nucleus from labeled proteins only for 4D in vivo imaging
Authors: Rieger B. , Molenaar C. , Dirks R.W. , Van Vliet L.J.
Published: August 2004

Studies of protein dynamics by 4D (3D + time) confocal microscopy in vivo are hampered by global cell motion. The time between the acquisitions of the 3D images is in the order of minutes. Therefore, it is not to be expected that the cell as a whole remains fixed in the water basin on the stage. This superimposes a motion on the protein dynamics that has to be removed. We present a robust registration technique to align the cell images that does not require the a priori establishment of point‐to‐point correspondences. Instead, it uses the distribution of the labeled proteins. After correction for the translation, the 3D rotation of the cell is estimated. A robust intrinsic body coordinate system is constructed via the inertia tensor from the intensity distribution. By combining basis transformation to this intrinsic coordinate system, we can calculated the rotation matrix in a conceptual and computational straightforward manner. We have evaluated the performance of this approach in three experiments with human osteaosarcoma cells (U‐2 OS), where the nuclear proteins Histon H4 and PML were visualized. The PML is concentrated in several dozen nuclear spots. Expression of Histon H4 results in a total nuclear staining. The registration results for both channels computed independently are very similar. Practically, this means that only the labeled material needs to be observed and still registration of the cell as a whole can be achieved. Microsc. Res. Tech. 64:142–150, 2004. © 2004 Wiley‐Liss, Inc.
3D restoration with multiple images acquired by a modified conventional microscope
Authors: Vermolen B.J. , Garini Y. , Young I.T.
Published: August 2004

A problem in high magnification microscopy is the blurring in the imaging of an object. In this article, we demonstrate a restoration technique that simultaneously makes use of the confocal image and the wide‐field image. These images can be acquired by a modified conventional microscope. In front of the light‐source, there is an array of pinholes. There are no pinholes at the detection plane. Instead, one or more pixels from the CCD camera are used, where the pinholes would have been. Using all pixels gives the wide‐field image, but using a selected subset can give a confocal image. The array is used to speed up the process of acquiring the image. Note that the speed of acquisition is proportional to the number of pinholes. We show that the restoration from the two images can lead to a better result than using only one of the images. If this is the case, we show that a distance of 5 times the diameter of the pinholes can give the same results as a distance of 20 times after deconvolution. This offers an increase in acquisition time of a factor 16. Microsc. Res. Tech. 64:113–125, 2004. © 2004 Wiley‐Liss, Inc.
Optical‐sectioning improvement in two‐color excitation scanning microscopy
Authors: Ibáñez‐López Cristina , Escobar Isabel , Saavedra Genaro , Martínez‐Corral Manuel
Published: August 2004

We present a new beam‐shaping technique for two‐color excitation fluorescence microscopy. We show that by simply inserting a properly designed shaded‐ring filter in the illumination beam of smaller wavelength, it is possible to improve the effective optical sectioning capacity of such microscopes by 23%. Such an improvement is obtained at the expense of only a very small increasing of the overall energy in the point‐spread‐function sidelobes. The performance of this technique is illustrated by a numerical imaging simulation. Microsc. Res. Tech. 64:96–102, 2004. © 2004 Wiley‐Liss, Inc.
Applying spectral fingerprinting to the analysis of FRET images
Authors: Neher Richard A. , Neher Erwin
Published: August 2004

Förster resonance energy transfer (FRET) allows one to study interactions between two fluorescently labeled molecules (donors and acceptors) at distances on the order of 5 nm. Many studies have described methods of how to measure the efficiency of FRET. However, few have addressed the question of how fluorescence from unpaired donors and acceptors can be determined in addition to that from FRET‐pairs and how the signal‐to‐noise ratio (SNR) of such estimates depends on the presence of the partner species. Such knowledge, however, is essential for many biological applications, in which—after initial characterization of the spectral properties of a well‐defined donor‐acceptor complex—the in vivo affinity and stoichiometry of the complex is of interest. Here, we provide a theoretical analysis on how spectral fingerprinting can be applied to separate fluorescence of FRET pairs from that originating from unpaired donors and acceptors and how to select imaging parameters to optimize the SNR of the estimates. Thereby, we uncover a fundamental problem in this application and discuss ways to evade its adverse consequences. We compare the expected resolution of traditional FRET measures with that of optimized spectral fingerprinting and analyze the resolution of a method for FRET measurements that combines spectral with fluorescence lifetime information. Microsc. Res. Tech. 64:185–195, 2004. © 2004 Wiley‐Liss, Inc.
Optimization of the extraction of paclitaxel from Taxus baccata L. by the use of microwave energy
Authors: Talebi Mohammad , Ghassempour Alireza , Talebpour Zahra , Rassouli Ali , Dolatyari Lila
Published: August 2004

A simple and rapid microwave‐assisted extraction (MAE) procedure was developed and optimized for the extraction of paclitaxel (Taxol®) from the needles of yew trees Taxus baccata L. grown in Iranian habitats. The samples, immersed in a methanol‐water mixture, were irradiated with microwaves in a closed‐vessel system. The method was evaluated using a factorial design approach based on parameters such as extraction time, temperature, methanol concentration in water (v/v), and the ratio of grams of sample to 10 mL of solvent. Statistical treatment of the results revealed that the selected parameters were all significant except the extraction time. Optimum conditions would be 1.5 g samples in 10 mL solvent (90% methanol), an extraction temperature of 95°C, and an extraction time of 7 min. The extracts has been analyzed by reverse‐phase high‐performance liquid chromatography with UV detection (LC/UV) at 227 nm for quantification. Liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) was used for confirmation. The main advantage of the proposed MAE method versus conventional solvent extraction (CSE) are the considerable reductions in time (7 min versus 16 h) and in solvent consumption (20 mL versus 150 mL). The MAE procedure yielded extracts that could be analyzed directly without any preliminary clean‐up or solvent exchange steps. Both extraction methods show RSDs lower than 10% and lead to comparable recoveries of paclitaxel (87–92%).
Association Behavior between End‐Functionalized Block Copolymers PEO‐PPO‐PEO and Poly(acrylic acid)
Authors: Wang Ying , Goethals Eric J. , Du Prez Filip E.
Published: August 2004

Summary: The end groups of ABA‐triblock copolymers HO–PEO–PPO–PEO–OH, (PEO – poly(ethylene oxide), PPO – poly(propylene oxide)), have been modified with ammonia, ethylene diamine and linear polyethylenimine (LPEI) by substitution of the α,ω‐ditosyl ester of the triblock copolymer (TsO–PEO–PPO–PEO–OTs) with amines, or by the hydrolysis of the corresponding poly(2‐methyl‐2‐oxazoline) (PMeOx) containing ABCBA block copolymers. The latter block copolymer structures have been obtained by the polymerization of MeOx using TsO–PEO–PPO–PEO–OTs as a macro‐initiator. Adding poly(acrylic acid) (PAA) to these (poly)amine terminated block copolymers leads to the formation of networks through a combination of PAA–PEO hydrogen bonding and PAA–(poly)amine acid‐base reaction. Depending on the number of amino groups at both chain ends of the block copolymer, the corresponding complexes behave as liquids, gels or precipitates. Introduction of as little as 1–5 wt.‐% block copolymers H2N–PEO–PPO–PEO–NH2 or H2NCH2CH2NH–PEO–PPO–PEO–NHCH2CH2NH2 to the system of HO–PEO–PPO–PEO–OH/PAA leads to viscous liquids with strong shear‐thickening behavior.

Reversible gel formation via the ternary PAA/HO–PEO–PPO–PEO–OH/H2N–PEO–PPO–PEO–NH2 system under shear conditions.

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Reversible gel formation via the ternary PAA/HO–PEO–PPO–PEO–OH/H2N–PEO–PPO–PEO–NH2 system under shear conditions.
High‐Molecular‐Weight Isobutene–Isoprene Copolymers Containing Unusually High Isoprene Content
Authors: McInenly Paula J. , Drewitt Mark J. , Baird Michael C.
Published: August 2004

Summary: The 1:2 adduct of the highly electrophilic borane B(C6F5)3 with n‐decanoic (stearic) acid, [n‐C17H35CO2H][B(C6F5)3]2 exhibits sufficiently enhanced acidity that it is an excellent initiator for the carbocationic copolymerization of isobutene with isoprene in methylene chloride and methyl chloride. High conversions to gel free, high‐molecular‐weight copolymers containing up to 15 wt.‐% isoprene are readily obtained, consistent with the anion [n‐C17H35CO2{BC6F5)3}2]− being very weakly coordinating. Thus chain transfer following IP incorporation into the growing polymeric chain, which normally results in low average molecular weights, is much less of a factor here.

The acidic 1:2 adduct of B(C6F5)3 with n‐decanoic acid, [n‐C17H35CO2H][B(C6F5)3]2, as an initiator for the carbocationic copolymerization of isobutene with isoprene.

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The acidic 1:2 adduct of B(C6F5)3 with n‐decanoic acid, [n‐C17H35CO2H][B(C6F5)3]2, as an initiator for the carbocationic copolymerization of isobutene with isoprene.
Index sets for computable differential equations
Authors: Cenzer Douglas , Remmel Jeffrey B.
Published: August 2004

Index sets are used to measure the complexity of properties associated with the differentiability of real functions and the existence of solutions to certain classic differential equations. The new notion of a locally computable real function is introduced and provides several examples of Σ04 complete sets. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Two constructive embedding‐extension theorems with applications to continuity principles and to Banach‐Mazur computability
Authors: Bauer Andrej , Simpson Alex
Published: August 2004

We prove two embedding and extension theorems in the context of the constructive theory of metric spaces. The first states that Cantor space embeds in any inhabited complete separable metric space (CSM) without isolated points, X, in such a way that every sequentially continuous function from Cantor space to ℤ extends to a sequentially continuous function from X to ℝ. The second asserts an analogous property for Baire space relative to any inhabited locally non‐compact CSM. Both results rely on having careful constructive formulations of the concepts involved.

As a first application, we derive new relationships between “continuity principles” asserting that all functions between specified metric spaces are pointwise continuous. In particular, we give conditions that imply the failure of the continuity principle “all functions from X to ℝ are continuous”, when X is an inhabited CSM without isolated points, and when X is an inhabited locally non‐compact CSM. One situation in which the latter case applies is in models based on “domain realizability”, in which the failure of the continuity principle for any inhabited locally non‐compact CSM, X, generalizes a result previously obtained by Escardó and Streicher in the special case X = C[0, 1].

As a second application, we show that, when the notion of inhabited complete separable metric space without isolated points is interpreted in a recursion‐theoretic setting, then, for any such space X, there exists a Banach‐Mazur computable function from X to the computable real numbers that is not Markov computable. This generalizes a result obtained by Hertling in the special case that X is the space of computable real numbers. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Approximation representations for reals and their wtt‐degrees
Authors: Barmpalias George
Published: August 2004

We study the approximation properties of computably enumerable reals. We deal with a natural notion of approximation representation and study their wtt‐degrees. Also, we show that a single representation may correspond to a quite diverse variety of reals. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Density and Baire category in recursive topology
Authors: Kalantari Iraj , Welch Larry
Published: August 2004

We develop the concepts of recursively nowhere dense sets and sets that are recursively of first category and study closed sets of points in light of Baire's Category Theorem. Our theorems are primarily concerned with exdomains (i. e. complements of domains) of recursive quantum functions and hence with avoidable points (i. e. points that can be forced into exdomains of recursive quantum functions). An avoidance function is a recursive function which can be used to expel avoidable points from domains of recursive quantum functions. We define an avoidable set of points to be an arbitrary subset of the avoidable points of a single avoidance function, and we study an effective union of such sets which we call a piecemeal avoidable set. We note that each of ‘the set of recursive points’ and ‘the set of avoidable points’ is of first category but not recursively of first category. We show an exdomain exists which is recursively nowhere dense, as well as one that is nowhere dense but not recursively nowhere dense. After establishing that every exdomain is recursively of first category, we prove that given any fixed exdomain, there is another exdomain, which while dense in the underlying space, is disjoint from the fixed exdomain. Finally, we show how to build a recursive sequence of recursive quantum functions that have mutually disjoint, dense exdomains. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Computable operators on regular sets
Authors: Ziegler Martin
Published: August 2004

For regular sets in Euclidean space, previous work has identified twelve ‘basic’ computability notions to (pairs of) which many previous notions considered in literature were shown to be equivalent. With respect to those basic notions we now investigate on the computability of natural operations on regular sets: union, intersection, complement, convex hull, image, and pre‐image under suitable classes of functions. It turns out that only few of these notions are suitable in the sense of rendering all those operations uniformly computable. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)