bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractHeat 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

AbstractToll‐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

AbstractInterleukin (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

AbstractTrophic 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

AbstractWe 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

AbstractThe 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

Abstract40Ar/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

AbstractGeomorphology 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

AbstractTwo 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

AbstractWe 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

AbstractIn 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

AbstractSodium 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

AbstractReceptor 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

AbstractMicroscopy 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

AbstractColocalization 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

AbstractThere 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

AbstractThe 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.