bluuebunny/crossref_metadata_2025_split huggingface dataset:
Attaining exponential convergence for the flux error with second‐ and fourth‐order accurate finite‐difference equations. I. Presentation of the basic concept and application to a pure diffusion system
Authors: Rudolph Manfred 
Published: March 2005

AbstractIt is a well‐known phenomenon called superconvergence in the mathematical literature that the error level of an integral quantity can be much smaller than the magnitude of the local errors involved in the computation of this quantity. When discretizing an integrated form of Fick's second law of diffusion the local errors reflect the accuracy of individual concentration points while the integral quantity has the physical meaning of the flux. This article demonstrates how an extraordinary fast exponential convergence towards zero can be achieved for the simulated flux error on the basis of finite–difference approximations that are only second‐order (Box 2 method) or fourth‐order (Box 4 method) accurate as far as the level of local errors is concerned. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 619–632, 2005
Attaining exponential convergence for the flux error with second‐ and fourth‐order accurate finite‐difference equations. II. Application to systems comprising first‐order chemical reactions
Authors: Rudolph Manfred 
Published: March 2005

AbstractThis article demonstrates that exponential convergence of the flux error can be achieved for any kinetic–diffusion system comprising an arbitrary number of (pseudo) first‐order chemical reactions if the underlying PDEs are discretized as outlined for the box 2 or box 4 method in the preceding part of this article. By investigating the eigenvalues and eigenvectors of the first‐order kinetic coupling matrix in general form the present article demonstrates that the simulation of any multispecies first‐order kinetic diffusion system can be as accurately done as the simulation of a single representative one‐species system. The Fourier coefficients governing the error level of the flux are much smaller in the limiting case of kinetic control as those reported in the preceding article for the limiting case of diffusion control. The higher rate of exponential convergence predicted on the basis of the mathematical model has been fully verified by the numerical results. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 633–641, 2005
Orthogonal designs, self‐dual codes, and the Leech lattice
Authors: Harada Masaaki , Kharaghani Hadi 
Published: March 2005

AbstractSymmetric designs and Hadamard matrices are used to construct binary and ternary self‐dual codes. Orthogonal designs are shown to be useful in construction of self‐dual codes over large fields. In this paper, we first introduce a new array of order 12, which is suitable for any set of four amicable circulant matrices. We apply some orthogonal designs of order 12 to construct new self‐dual codes over large finite fields, which lead us to the odd Leech lattice by Construction A. © 2005 Wiley Periodicals, Inc. J Combin Designs 13: 184–194, 2005.
Smart materials as scaffolds for tissue engineering
Authors: Rosso Francesco , Marino Gerardo , Giordano Antonio , Barbarisi Manlio , Parmeggiani Domenico , Barbarisi Alfonso 
Published: March 2005

AbstractIn this review, we focused our attention on the more important natural extracellular matrix (ECM) molecules (collagen and fibrin), employed as cellular scaffolds for tissue engineering and on a class of semi‐synthetic materials made from the fusion of specific oligopeptide sequences, showing biological activities, with synthetic materials. In particular, these new “intelligent” scaffolds may contain oligopeptide cleaving sequences specific for matrix metalloproteinases (MMPs), integrin binding domains, growth factors, anti‐thrombin sequences, plasmin degradation sites, and morphogenetic proteins. The aim was to confer to these new “intelligent” semi‐synthetic biomaterials, the advantages offered by both the synthetic materials (processability, mechanical strength) and by the natural materials (specific cell recognition, cellular invasion, and the ability to supply differentiation/proliferation signals). Due to their characteristics, these semi‐synthetic biomaterials represent a new and versatile class of biomimetic hybrid materials that hold clinical promise in serving as implants to promote wound healing and tissue regeneration. © 2005 Wiley‐Liss, Inc.
Diverse isoforms of colony‐stimulating factor‐1 have different effects on the development of stroma‐dependent hematopoietic cells
Authors: Friel Jutta , Heberlein Christoph , Geldmacher Maren , Ostertag Wolfram 
Published: March 2005

AbstractMaintenance and differentiation of hematopoietic stem and progenitor cells are controlled by complex interactions with the stroma microenvironment. Stroma–cell interactions can be supported by locally expressed membrane‐spanning cell‐surface (cs) growth factors. CSF‐1 is expressed by stroma as a soluble glycoprotein, as proteoglycan, or as a membrane‐spanning cs glycoprotein. CSF‐1 regulates the survival, proliferation, and differentiation of mononuclear phagocytes. Whereas the biological role of soluble CSF‐1 is well characterized, the function of the membrane‐spanning cell‐surface CSF‐1 (csCSF‐1) remains unclear. To analyze the biological significance of csCSF‐1 in vitro, we used an epithelial cell line to ectopically express the different CSF‐1 isoforms. In co‐cultures of CSF‐1 transduced epithelial cells with primary, early hematopoietic progenitor cells we examined whether interaction between csCSF‐1 and its receptor mediates cell proliferation, self‐renewal, or differentiation. csCSF‐1 induces long‐lasting proliferation of stimulated cells and furthermore supports self‐renewal. Ectopic secretion of soluble CSF‐1 does not permit long‐term growth of progenitor cells but induces differentiation of monocytes into macrophages. Previously, we showed that the soluble and cs isoforms of stroma‐encoded SCF differently affect the development of hematopoietic cells. Cell‐surface SCF (csSCF) promotes self‐renewal of stimulated cells whereas soluble SCF causes clonal extinction. These results and those presented here for CSF‐1 provide evidence for diverse functions of the isoforms of the ligands SCF and CSF‐1 for two tyrosine kinase receptors of the subclass III both regulating hematopoiesis on stroma. J. Cell. Physiol. 204: 247–259, 2005. © 2005 Wiley‐Liss, Inc.
Identification of in vivo P‐glycoprotein mRNA decay intermediates in normal liver but not in liver tumors
Authors: Lee Chow H. , Rehaume Vicki E. , Shandro Janis 
Published: March 2005

AbstractPost‐transcriptional regulation at the level of mRNA stability is one important mechanism for over‐expression of P‐glycoprotein (Pgp) genes observed in cultured cells and in animals. A previous study has shown that mRNA half‐lives for Pgp genes in normal liver were less than 2 h, in contrast to greater than 12 h measured in a transplantable liver tumor line. This lower turnover rate of Pgp mRNA may, in large part, contribute to the abundance of Pgp mRNA in liver tumors. The current study sought to investigate the underlying mechanism for the lower turnover rate of Pgp2 mRNA previously determined in liver tumors. As a first approach, we set out to understand the Pgp2 mRNA decay in both normal liver and liver tumors by first identifying and characterizing Pgp2 mRNA degradation intermediates. In this study, we showed that the sensitive ligation‐mediated polymerase chain reaction (LM‐PCR) method can be used to detect a homogenous pool of in vitro transcribed RNA down to 0.4 ng. By employing gene‐specific primers in the LM‐PCR method, we successfully identified four Pgp2 mRNA decay intermediates in normal liver. All four decay intermediates detected correspond to the 5′ coding region of Pgp2 mRNA, and surprisingly no decay intermediates which correspond to 3′ untranslated region, 3′ coding region or middle coding region were found using LM‐PCR. The identified decay intermediates are unique to the normal liver as they were absent or present at very low level in all three liver tumor samples analyzed. This observation supports our previous findings that the Pgp mRNA turnover rate is lower in liver tumors than in normal liver. These findings have implications for our understanding of the regulation of Pgp mRNA turnover in normal and malignant tissues. © 2005 Wiley‐Liss, Inc.
Regulatory networks for the control of body iron homeostasis and their dysregulation in HFE mediated hemochromatosis
Authors: Ludwiczek Susanne , Theurl Igor , Bahram Siamak , Schümann Klaus , Weiss Günter 
Published: March 2005

AbstractAlthough the recent identification of several genes has extended our knowledge on the maintenance of body iron homeostasis, their tissue specific expression patterns and the underlying regulatory networks are poorly understood. We studied C57black/Sv129 mice and HFE knockout (HFE −/−) variants thereof as a model for hemochromatosis, and investigated the expression of iron metabolism genes in the duodenum, liver, and kidney as a function of dietary iron challenge. In HFE +/+ mice dietary iron supplementation increased hepatic expression of hepcidin which was paralleled by decreased iron regulatory protein (IRP) activity, and reduced expression of divalent metal transporter‐1 (DMT‐1) and duodenal cytochrome b (Dcytb) in the enterocyte. In HFE −/− mice hepcidin formation was diminished upon iron challenge which was associated with decreased hepatic transferrin receptor (TfR)‐2 levels. Accordingly, HFE −/− mice presented with high duodenal Dcytb and DMT‐1 levels, and increased IRP and TfR expression, suggesting iron deficiency in the enterocyte and increased iron absorption. In parallel, HFE −/− resulted in reduced renal expression of Dcytb and DMT‐1. Our data suggest that the feed back regulation of duodenal iron absorption by hepcidin is impaired in HFE −/− mice, a model for genetic hemochromatosis. This change may be linked to inappropriate iron sensing by the liver based on decreased TfR‐2 expression, resulting in reduced circulating hepcidin levels and an inappropriate up‐regulation of Dcytb and DMT‐1 driven iron absorption. In addition, iron excretion/reabsorption by the kidneys may be altered, which may aggravate progressive iron overload. © 2005 Wiley‐Liss, Inc.
D‐aspartate modulates transcriptional activity in Harderian gland of frog, Rana esculenta: Morphological and molecular evidence
Authors: Raucci Franca , Santillo Alessandra , D'Aniello Antimo , Chieffi Paolo , Baccari Gabriella Chieffi 
Published: March 2005

AbstractIn the green frog, Rana esculenta, a substantial amount of D‐aspartate (D‐Asp) is found endogenously within the Harderian gland (HG) following its synthesis from L‐aspartate (L‐Asp) by an aspartate racemase. The frog HG is an orbital seromucoid gland that displays seasonal changes in secretory activity. Our in vivo experiments, consisting of i.p. injection of 2.0 μmol/g b.w. D‐Asp in frogs collected during two periods of differing glandular activity (high or medium‐low secretory activity), revealed that HG can to take up and accumulate D‐Asp and that this amino acid may modulate the exocrine secretion through a kinase pathway. At a time when the gland shows relatively low secretory activity, i.p. administration of D‐Asp rapidly induced activation of ERK1 and an increase in cells active in RNA synthesis. This increase in transcriptional activity was followed by a significant increase in mucous secretion. By contrast, administration of exogenous D‐Asp when HG was showing high activity rapidly induced inhibition of both ERK1 and transcriptional activity. Since D‐Asp is known to be recognized by receptors for N‐methyl‐D‐aspartic acid (NMDA), it is possible that in the HG, D‐Asp mediated NMDA activation may enhance the kinase pathway. The above activation of opposing stimulatory and inhibitory processes could reflect different levels of NMDA‐receptor activity, which could vary as a function of the level of gland activity. This study provides the first evidence of a role for this excitatory amino acid in exocrine secretion. The effects of D‐Asp in HG appear to be specific since they were not seen in frogs treated with other D‐ or L‐amino acids with known excitatory effects on neurosecretion. © 2005 Wiley‐Liss, Inc.
Regulatory and necrotic volume increase in boar spermatozoa
Authors: Petrunkina A.M. , Jebe E. , Töpfer‐Petersen E. 
Published: March 2005

AbstractSpermatozoa of many species initially respond to hypotonicity as perfect osmometers. Thereafter they undergo a regulatory process resulting in a decrease in cell volume, similar to that reported for somatic cells. Regulatory volume increase (RVI), a complementary process which is assumed to occur following initial shrinkage of sperm volume after exposure to a hypertonic medium, has not yet been described in detail for spermatozoa. In this study, we investigated whether spermatozoa are able to regulate their volume after hypertonic stress and whether this ability is maintained in preserved sperm. Cell volume changes were recorded using electronic cell sizing. Sperm response to the ion channels blockers quinidine, tamoxifen, and dydeoxyforskolin, and to protein kinase/phosphatase inhibitors lavendustin, staurosporine, and vanadate was studied to investigate possible mechanisms of RVI. Annexin V staining was used in combination with propidium iodide to determine whether hypertonic stress may induce apoptosis. Overall protein tyrosine phosphorylation under hypertonic conditions was measured via flow cytometry using antiphosphotyrosine antibody. Spermatozoa exposed to hypertonic stress initially responded with an abundant subpopulation according to the perfect osmometer model and recovered their volume from this shrinkage after 20 min. RVI was inhibited by quinidine and tamoxifen, which indicates the involvement of the important cellular ions sodium and chloride in this process. Volume regulatory ability was essentially maintained during storage of liquid semen. However, the response of the sperm population was heterogeneous. A second population raised, containing spermatozoa with larger volumes, which demonstrated irregularities in the volume response with respect to osmotic challenge, ion channel blockers, and storage. Under hypertonic conditions, both protein kinase inhibitors (PKI) led to increased isotonic volumes and to elevated initial relative volumes and subsequent volume decrease. RVI was inhibited by the vanadate. Hypertonic stress did not result in an increase in early apoptotic cells, but produced a shift toward late necrotic cells. Substitution of sodium and chloride by choline and sulfate resulted in decreased isotonic volume of sperm treated with lavendustin. Tyrosine phosphorylation levels were reduced after 20 min under hypertonic conditions. It was concluded that RVI is regulated via a protein tyrosine kinase‐dependent pathway, and that dephosphorylation occurs when volume regulation is required. The necrotic volume increase (NVI) is associated with the accumulation of sodium and chloride following uncontrolled opening of the channels. The ability to regulate volume after exposure to hypertonic conditions is important for sperm functionality and can have practical applications in spermatological diagnostics and cryopreservation. © 2005 Wiley‐Liss, Inc.
Stem cells and pulmonary metamorphosis: New concepts in repair and regeneration
Authors: Aliotta Jason M. , Passero Michael , Meharg Joseph , Klinger James , Dooner Mark S. , Pimentel Jeffrey , Quesenberry Peter J. 
Published: March 2005

AbstractAdult stem cells are likely to have much more versatile differentiation capabilities than once believed. Numerous studies have appeared over the past decade demonstrating the ability of adult stem cells to differentiate into a variety of cells from non‐hematopoietic organs, including the lung. The goal of this review is to provide an overview of the growth factors which are thought to be involved in lung development and disease, describe the cells within the lung that are believed to replace cells that have been injured, review the studies that have demonstrated the transformation of bone marrow‐derived stem cells into lung cells, and describe potential clinical applications with respect to human pulmonary disease. © 2005 Wiley‐Liss, Inc.
Characterization of five evolutionary conserved regions of the human tyrosine hydroxylase (TH) promoter: Implications for the engineering of a human TH minimal promoter assembled in a self‐inactivating lentiviral vector system
Authors: Romano Gaetano , Suon Sokreine , Jin Hao , Donaldson Angela E. , Iacovitti Lorraine 
Published: March 2005

AbstractA DNA fragment of about 13 kb containing the human tyrosine hydroxylase (TH) promoter was previously isolated from a genomic DNA library and sequenced. The 11 kb from the transcription start of the human TH promoter was successively joined to the green fluorescent protein (GFP) to generate a transgenic mouse model. High levels of GFP expression could be observed in TH‐positive cells of the Substantia nigra of embryonic and adult mice. Intriguingly, the sequence of the human TH promoter showed a low degree of homology with the mouse and rat TH promoters. In fact, comparative analysis of the sequences of human, rat, and mouse TH promoters revealed only five small regions of high homology. These five evolutionarily conserved regions were numbered in numeric progression from the 5′ end of human TH promoter. In the present study, a panel of minimal human TH promoters was generated to analyze the transcriptional activity and specificity of gene expression conferred by the five conserved regions (CRs). The series of constructs was termed 250 bp and contained the first −194 bp of the human TH promoter immediately upstream of the transcription start, the first 35 bp the human TH messenger RNA leader, plus one or more of the five CRs. All the constructs were assembled in a self‐inactivating form of the latest series of lentiviral vector system based on the human immunodeficiency virus type 1 (HIV‐1). Lentiviral‐mediated gene transfer was highly efficient for the in vitro transduction of human neuronal progenitor cells (hNPCs). Since a subset of hNPCs express TH following in vitro treatment with a mixture of differentiating agents, it was possible to assess specificity of expression for all the minimal human TH promoters. Overall, the successive addition of the five conserved regions produced a greater degree of specificity in induced TH‐positive hNPCs, in particular after the addition of CRI (−8,917, −8,876). However, the human TH minimal promoters did not show any specificity for TH‐positive differentiated mouse primary striatal and S. nigra cells, indicating a difference of TH gene regulation between the human and mouse systems. The human TH minimal promoters may provide the opportunity for the selection of TH‐positive human embryonic and adult stem cells for brain transplantation experiments in animal models for Parkinson's disease. © 2005 Wiley‐Liss, Inc.
Three‐dimensional culture of melanoma cells profoundly affects gene expression profile: A high density oligonucleotide array study
Authors: Ghosh Sourabh , Spagnoli Giulio C. , Martin Ivan , Ploegert Sabine , Demougin Philippe , Heberer Michael , Reschner Anca 
Published: March 2005

AbstractGrowth in three‐dimensional (3D) architectures has been suggested to play an important role in tumor expansion and in the resistance of cancers to treatment with drugs or cytokines or irradiation. To obtain an insight into underlying molecular mechanisms, we addressed gene expression profiles of NA8 melanoma cells cultured in bidimensional monolayers (2D) or in 3D multicellular tumor spheroids (MCTS). MCTS containing 10‐30,000 cells were generated upon overnight culture in poly‐Hydroxyethylmethacrylate (polyHEMA) coated plates. Kinetics of cell proliferation in MCTS was significantly slower than in monolayer cultures. Following long‐term culture (>10 days), however, MCTS showed highly compact and organised cell growth in outer layers, with necrotic cores. Oligonucleotide microarray analysis of the expression of over 20,000 genes was performed on cells cultured in standard 2D, in the presence of collagen as model of extracellular matrix (ECM), or in MCTS. Gene expression profiles of cells cultured in 2D in the presence or absence of ECM were highly similar, with ≥threefold differences limited to five genes. In contrast, culture in MCTS resulted in the significant, ≥threefold, upregulation of the expression of >100 transcripts while 73 were ≥threefold downregulated. In particular, genes encoding CXCL1, 2, and 3 (GRO‐α, ‐β, and γ), IL‐8, CCL20 (MIP‐3α), and Angiopoietin‐like 4 were significantly upregulated, whereas basic FGF and CD49d encoding genes were significantly downregulated. Oligonucleotide chip data were validated at the gene and protein level by quantitative real‐time PCR, ELISA, and cell surface staining assays. Taken together, our data indicate that structural modifications of the architecture of tumor cell cultures result in a significant upregulation of the expression of a number of genes previously shown to play a role in melanoma progression and metastatic process. © 2005 Wiley‐Liss, Inc.
Effects of development and iron status on ceruloplasmin expression in rat brain
Authors: Chang Yan Zhong , Qian Zhong Ming , Wang Kui , Zhu Li , Yang Xiao Da , Du Jin Rong , Jiang Lin , Ho Kwok Ping , Wang Qin , Ke Ya 
Published: March 2005

AbstractThe increased iron content in the brain of subjects with aceruloplasminemia has implicated ceruloplasmin (CP) as a major factor in the regulation of regional brain iron content. In this study, we investigated the effects of age and iron on CP expression in rat brain. In all four regions, the iron concentrations increased with developmental age. There is a similar trend in age‐induced changes in CP mRNA and protein. The CP mRNA and protein levels were both lowest at postnatal day (PND) 7. The expression increased gradually with age, reaching the highest at PND196 in the striatum and substantia nigra, and at PND21 and PND63 in the cortex and hippocampus, respectively. This suggests the existence of an age‐dependent pre‐transcriptional regulation and a regionally specific effect of age on CP expression in the brain. Although total iron in all four regions was significantly lower in the rats fed with a low‐iron diet for 6 weeks and higher in the rats with a high‐iron diet than those in the control animals, no significant between‐group differences in CP mRNA and protein were found in these animals, except in the substantia nigra where a significant increase in CP protein in high‐iron rats was observed, and the reverse in low‐iron rats. These findings suggested that the effects of iron on CP expression in the brain may be region‐specific, and that regulation of CP expression by iron in the substantia nigra was at the post‐transcriptional level. © 2005 Wiley‐Liss, Inc.