bluuebunny/crossref_metadata_2025_split huggingface dataset:
Furin Processing and Proteolytic Activation of Semliki Forest Virus
Authors: Zhang Xinyong , Fugère Martin , Day Robert , Kielian Margaret 
Published: February 2003

ABSTRACT
The alphavirus Semliki Forest virus (SFV) infects cells via a low-pH-dependent membrane fusion reaction mediated by the E1 envelope protein. Fusion is regulated by the interaction of E1 with the receptor-binding protein E2. E2 is synthesized as a precursor termed “p62,” which forms a stable heterodimer with E1 and is processed late in the secretory pathway by a cellular furin-like protease. Once processing to E2 occurs, the E1/E2 heterodimer is destabilized so that it is more readily dissociated by exposure to low pH, allowing fusion and infection. We have used FD11 cells, a furin-deficient CHO cell line, to characterize the processing of p62 and its role in the control of virus fusion and infection. p62 was not cleaved in FD11 cells and cleavage was restored in FD11 cell transfectants expressing human furin. Studies of unprocessed virus produced in FD11 cells (wt/p62) demonstrated that the p62 protein was efficiently cleaved by purified furin in vitro, without requiring prior exposure to low pH. wt/p62 virus particles were also processed during their endocytic uptake in furin-containing cells, resulting in more efficient virus infection. wt/p62 virus was compared with mutant L, in which p62 cleavage was blocked by mutation of the furin-recognition motif. wt/p62 and mutant L had similar fusion properties, requiring a much lower pH than control virus to trigger fusion and fusogenic E1 conformational changes. However, the in vivo infectivity of mutant L was more strongly inhibited than that of wt/p62, due to additional effects of the mutation on virus-cell binding.
Restriction of Human Immunodeficiency Virus Type 1 Rev Function in Murine A9 Cells Involves the Rev C-Terminal Domain
Authors: Marques Sandra M. P. , Veyrune Jean-Luc , Shukla Ram R. , Kumar Ajit 
Published: February 2003

ABSTRACTThe human immunodeficiency virus type 1 (HIV-1) Rev and human T-cell leukemia virus type 1 (HTLV-1) Rex proteins are essential for the expression of viral structural proteins and productive infection. Both contain a nuclear export signal (NES) in their C-terminal domain and a nuclear localization signal (NLS) in their N-terminal domain. The NES and NLS are necessary for shuttling between nucleus and cytoplasm and are therefore indispensable for the transport of unspliced and singly spliced viral transcripts. HIV-1 Rev function is restricted in A9 cells, a murine fibroblast cell line, whereas HTLV-1 Rex is functional in these cells. Immunofluorescence studies with RevGFP fusion protein demonstrate normal import and export of Rev in A9 cells. To ascertain which domains of Rev are necessary for the restriction of Rev function in A9 cells, we studied a chimeric construct in which the NES domain of Rev was exchanged with Rex C-terminal amino acids 79 to 95, the Rev1-79/Rex79-95 chimera, which restored Rev function in A9 cells. In addition, overexpression of a truncated Rev containing the Rev C-terminal domain in the presence of wild-type Rev, led to restoration of Rev function in A9 cells. These results suggest that the C-terminal domain of HIV-1 Rev plays an important role in restricting Rev function in murine cells.
Phase Separation in Metal Oxides
Authors: Rao C. N. R. , Vanitha P. V. , Cheetham Anthony K. 
Published: February 2003

AbstractA fascinating phenomenon, recently found to occur in certain transition‐metal oxides, is phase separation wherein pure, nominally monophasic oxides of transition metals with well‐defined compositions separate into two or more phases over a specific temperature range. Such phase separation is entirely reversible, and is generally the result of a competition between charge‐localization and ‐delocalization, the two situations being associated with contrasting electronic and magnetic properties. Coexistence of more than one phase, therefore, gives rise to electronic inhomogeneity and a diverse variety of magnetic, transport, and other properties, not normally expected of the nominal monophasic composition. An interesting feature of phase separation is that it covers a wide range of length scales anywhere between 1–200 nm. While cuprates and manganates, especially the latter, provide excellent examples of phase separation, it is possible that many other transition‐metal compounds with extended structures will be found to exhibit phase separation.
The Characterisation of Supported Platinum Nanoparticles on Carbon Used for Enantioselective Hydrogenation: A Combined Electrochemical–STM Approach
Authors: Attard Gary A. , Ahmadi Ahmad , Jenkins David J. , Hazzazi Omar A. , Wells Peter B. , Griffin Ken G. , Johnston Peter , Gillies Jennifer E. 
Published: February 2003

AbstractThe action of chiral modifiers like cinchonine and cinchonidine in facilitating enationselectivity in heterogeneous catalysis is investigated using a combination of electrochemical and scanning probe methods. The surface chirality of corner kink sites is suggested as being crucial for chirality recognition at supported catalyst nanoparticles. Other aspects of chirality in relation to one, two, three and four dimensions are also discussed.
Preparation, structure and thermal properties of CuGa5Se8
Authors: Orlova N. S. , Bodnar I. V. , Kushner T. L. 
Published: February 2003

AbstractThe structural parameters, the axial thermal expansion coefficients and the characteristic Debye temperatures for the order vacancy compound CuGa5Se8 with the chalcopyrite‐related structure, prepared by the Bridgman technique, were determined at different temperatures between 90 and 650 K by the X‐ray diffraction method. The melting point of this compound was defined from the differential thermal analysis data. The anisotropy of thermal expansion in CuGa5Se8 is shown to exist with the coefficients along a‐axis being larger than those along the c‐axis throughout the temperature range studied.
Diradical versus Concerted Mechanisms for the Dihydroxylation of Protoanemonin by OsO4 and OsO4−NH3 − The Effect of the Base in the Reaction
Authors: Ujaque Gregori , Maseras Feliu , Lledós Agustí 
Published: February 2003

AbstractThe dihydroxylation of a set of monosubstituted olefins [ethene (1), propene (2), styrene (3)] and 5‐methylene‐2(5H)‐furanone [protoanemonin (4)] by osmium tetroxide have been studied by means of DFT (B3LYP) calculations. The effect on the reaction mechanism of the coordination of a base (NH3) to OsO4 (5) to form OsO4−NH3 (6) has been investigated. These calculations show that the activation barriers for the [3+2] concerted mechanisms are lowered by the presence of an amine coordinating the osmium tetroxide, in agreement with experiment. For the dihydroxylation of protoanemonin (an olefin having a stepwise diradical mechanism in the Diels−Alder reaction) both the concerted and the diradical mechanisms have been evaluated. These studies indicate that the dihydroxylation of olefins proceeds through a concerted mechanism, although in the dihydroxylation of protoanemonin the diradical mechanism may play a significant role. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)
Knowledge sharing in cooperative research and development
Authors: Sakakibara Mariko 
Published: February 2003

AbstractThis article examines the effects of knowledge sharing or endogenous spillovers among R&D consortia participants on R&D competition when R&D enhances a firm's absorptive capacity. A three‐stage model illustrates how different compositions of R&D consortia affect endogenous spillover rates and R&D spending of participants. When consortium participants possess complementary knowledge, the model suggests that participation increases the degree of knowledge sharing and intensifies firms' R&D efforts to learn from other members compared with the case when no cooperation takes place. This type of R&D consortia is welfare enhancing, justifying government support for these projects. Copyright © 2003 John Wiley & Sons, Ltd.
Isotopic alteration of mammalian tooth enamel
Authors: Schoeninger M. J. , Hallin K. , Reeser H. , Valley John W. , Fournelle John 
Published: February 2003

AbstractMammalian tooth enamel carbonates from a Pliocene site at Allia Bay in northern Kenya show variable carbon and oxygen isotopic alteration. Sample screening by cathodoluminescence, prior to isotopic analysis, identified areas of extensive chemical alteration and others that were minimally altered. The luminescent patterns were used to guide sampling for the isotope study. Carbon stable isotope ratios of the apatite carbonate from luminescent enamel exteriors differ from the ratios in the enamel interiors and the magnitude of difference varies widely. The interior of the enamel usually retains the carbon isotope ratios expected based on faunal identification, but in a minority of cases, all of the enamel appears to be altered isotopically. Among fauna with an apparent mixed feeding signal, it is particularly difficult to determine whether the δ13C value is due to an actual mixed feeding strategy during life or to alteration toward sediment values. Palaeoecological reconstructions based on the δ13C values of enamel carbonate in browsing fauna would be affected, in many cases, since differences of 1‰ are significant for such reconstructions. Even so, careful selection of unaltered enamel sections should avoid this problem. Palaeodiet reconstruction would be less affected except in those cases where the alteration approaches 5‰. In such cases, a mixed feeding strategy would be the erroneous interpretation of the data. Oxygen isotope ratios in the enamel carbonates show no pattern and the retention of biogenic values is unlikely. For this reason, palaeotemperature reconstructions, based on the δ18O values of the enamel carbonate, would not be possible at this site. Copyright © 2003 John Wiley & Sons, Ltd.
What do stable isotopes tell us about hominid dietary and ecological niches in the pliocene?
Authors: Lee‐Thorp J. A. , Sponheimer M. , van der Merwe N. J. 
Published: February 2003

AbstractBy now a reasonable set of carbon and oxygen isotope data from tooth enamel has been accumulated for South African Plio‐Pleistocene hominids and associated fauna. Almost all individuals measured, independent of species and importantly, environment, show significant C4 dietary inputs with some individuals showing very substantial C4 inputs. This implies interactions with grassy environments for a period of well over a million years, a period that saw environments in southern Africa shift from closed woodlands to more open, grassy landscapes. Carbon isotope analysis alone is unable to permit the important distinction between direct consumption of grasses, or indirect consumption via grass‐eating animals, such as small vertebrates and invertebrates. Other chemical tools provide ambiguous results. For instance, hominid strontium/calcium distributions at Swartkrans have been interpreted as supporting omnivory, but other explanations are equally plausible. Relatively low oxygen isotope values for all hominids in comparison to associated fauna show similarities with suids, monkeys and carnivores, but the causes of these similarities are as yet poorly understood. On present evidence hominid interaction with grassland foods is secure although their exact nature remains elusive. Copyright © 2003 John Wiley & Sons, Ltd.
On bone collagen—apatite‐carbonate isotopic relationships
Authors: Hedges R. E. M. 
Published: February 2003

AbstractThis paper addresses possible underlying causes of the observed systematic spacings in the carbon isotopic composition of bone collagen and bone apatite‐carbonate when herbivores, omnivores and carnivores are compared. In particular it examines whether the observed systematic spacings are due to dietary differences, or to metabolic differences. It concludes that a simple model for diet‐to‐collagen isotopic fractionation (based on dietary difference) can account for half of the observed spacing, but probably not more than that. It also examines the role of methanogenesis and argues that this is a feasible explanation for ruminant and, to a lesser extent, hindgut fermenter, spacing values, although again it is difficult to account for the full amount observed. It also considers the implications of observations indicating that much of the change due to different diets in a given species is probably due to isotopic shifts in bone carbonate, rather than collagen. Copyright © 2003 John Wiley & Sons, Ltd.
Surface modification of a liquid‐crystalline polymer for copper metallization
Authors: Ge J. , Turunen M. P. K. , Kivilahti J. K. 
Published: February 2003

AbstractThe effects of different surface modifications on the adhesion of copper to a liquid‐crystalline polymer (LCP) were investigated with X‐ray photoelectron spectroscopy, scanning electron microscopy, atomic force microscopy, contact‐angle measurements, and pull tests. High pull‐strength values were achieved when copper was sputter‐deposited onto plasma and reactive‐ion‐etching (RIE)‐pretreated LCP surfaces. The values were comparable to the reference pull strengths obtained with laminated copper on the LCP. The adhesion was relatively insensitive to the employed feed gas in the pretreatments. The surface characterizations revealed that for RIE and plasma treatments, the enhanced adhesion was attributable to the synergistic effects of the increased surface roughness and polar component of the surface free energy of the polymer. However, if the electroless copper deposition was performed on RIE‐ or plasma‐treated surfaces, very poor adhesion was measured. Good adhesion between the LCP substrate and electrolessly deposited copper was achieved only in the case of wet‐chemical surface roughening as a result of the creation of a sufficient number of mechanical interlocking sites, together with a significant loss of oxygen functionalities, on the surface. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 623–636, 2003
An examination of the relationships between JIT and financial performance
Authors: Fullerton Rosemary R. , McWatters Cheryl S. , Fawson Chris 
Published: February 2003

AbstractDespite abundant information explaining the expected benefits from successful just‐in‐time (JIT) implementation, only tenuous validation of the linkage between financial performance and JIT exists. Managers act rationally in implementing JIT if they are convinced that JIT enhances firm performance. From both a cross‐sectional and longitudinal perspective, this survey study of 253 US manufacturing firms finds significant statistical relationships between measures of profitability and the degree of specific JIT practices used. The evidence provides empirical support to the premise that firms that implement and maintain JIT manufacturing systems will reap sustainable rewards as measured by improved financial performance.
Bone formation following transplantation of genetically modified primary bone marrow stromal cells
Authors: Sugiyama Osamu , Orimo Hideo , Suzuki Satoru , Yamashita Kazuo , Ito Hiromoto , Shimada Takashi 
Published: February 2003

AbstractBone marrow stromal cells contain mesenchymal stem cells that can differentiate into a variety of mesenchymal tissues; in the presence of BMP‐2, for example, they differentiate into osteoblasts. We constructed replication‐deficient adenoviral vectors encoding human BMP‐2 (BMP‐2/Ad) or BMP‐4 (BMP‐4/Ad) and used them to transduce primary bone marrow stromal cells from the femurs of four‐week‐old female C3H mice, which then expressed and processed functional BMP‐2 or BMP‐4 protein. Enzyme assays and histochemical staining showed both groups of cells to possess alkaline phosphatase activity, a marker of differentiation into osteoblasts, though the activity was higher in cells transduced with BMP‐2/Ad. When BMP‐2/Ad‐transduced cells were injected into the thigh muscles of immunocompetent C3H mice, ossicle development was detected on radiographs within four weeks after injection. Moreover, histological analysis indicated that newly developed ossicles contain mature osseous components, including cortical bone and bone marrow, within eight weeks. Thus, syngeneic transplantation of genetically modified primary bone marrow stromal cells induced bone formation in immunocompetent mice, perhaps indicating its potential for use in the development of therapeutic protocols aimed at enhancing bone formation. © 2003 Orthopaedic Research Society. Published by Elsevier Science Ltd. All rights reserved.
Identifying differentially expressed genes using
false discovery rate controlling procedures
Authors: Reiner Anat , Yekutieli Daniel , Benjamini Yoav 
Published: February 2003

Abstract
Motivation: DNA microarrays have recently been used for the purpose of monitoring expression levels of thousands of genes simultaneously and identifying those genes that are differentially expressed. The probability that a false identification (type I error) is committed can increase sharply when the number of tested genes gets large. Correlation between the test statistics attributed to gene co-regulation and dependency in the measurement errors of the gene expression levels further complicates the problem. In this paper we address this very large multiplicity problem by adopting the false discovery rate (FDR) controlling approach. In order to address the dependency problem, we present three resampling-based FDR controlling procedures, that account for the test statistics distribution, and compare their performance to that of the naïve application of the linear step-up procedure in Benjamini and Hochberg (1995). The procedures are studied using simulated microarray data, and their performance is examined relative to their ease of implementation.
Results: Comparative simulation analysis shows that all four FDR controlling procedures control the FDR at the desired level, and retain substantially more power then the family-wise error rate controlling procedures. In terms of power, using resampling of the marginal distribution of each test statistics substantially improves the performance over the naïve one. The highest power is achieved, at the expense of a more sophisticated algorithm, by the resampling-based procedures that resample the joint distribution of the test statistics and estimate the level of FDR control.
Availability: An R program that adjusts p-values using FDR controlling procedures is freely available over the Internet at www.math.tau.ac.il/~ybenja
Contact: anatr@post.tau.ac.il
* To whom correspondence should be addressed.
Identification of key concepts in biomedical literature using a modified Markov heuristic
Authors: Majoros W. H. , Subramanian G. M. , Yandell M. D. 
Published: February 2003

Abstract
Motivation: The recent explosion of interest in mining the biomedical literature for associations between defined entities such as genes, diseases and drugs has made apparent the need for robust methods of identifying occurrences of these entities in biomedical text. Such concept-based indexing is strongly dependent on the availability of a comprehensive ontology or lexicon of biomedical terms. However, such ontologies are very difficult and expensive to construct, and often require extensive manual curation to render them suitable for use by automatic indexing programs. Furthermore, the use of statistically salient noun phrases as surrogates for curated terminology is not without difficulties, due to the lack of high-quality part-of-speech taggers specific to medical nomenclature.
Results: We describe a method of improving the quality of automatically extracted noun phrases by employing prior knowledge during the HMM training procedure for the tagger. This enhancement, when combined with appropriate training data, can greatly improve the quality and relevance of the extracted phrases, thereby enabling greater accuracy in downstream literature mining tasks.
Contact: bmajoros@tigr.org
* To whom correspondence should be addressed.
Endoproteolytic Processing of the Lymphocytic Choriomeningitis Virus Glycoprotein by the Subtilase SKI-1/S1P
Authors: Beyer Winfried R. , Pöpplau Dennis , Garten Wolfgang , von Laer Dorothee , Lenz Oliver 
Published: February 2003

ABSTRACT

The envelope glycoprotein (GP) of lymphocytic choriomeningitis virus (LCMV) is posttranslationally cleaved into two subunits. We show here that this endoproteolytic processing is not required for transport to the cell surface but is essential for LCMV GP to mediate infectivity of pseudotyped retroviral vectors. By systematic mutational analysis of the LCMV GP cleavage site, we determined that the consensus motif R-(R/K/H)-L-(A/L/S/T/F)
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is essential for the endoproteolytic processing. In agreement with the identified consensus motif, we show that the cellular subtilase SKI-1/S1P cleaves LCMV GP.
N-Linked Glycosylation and Sequence Changes in a Critical Negative Control Region of the ASCT1 and ASCT2 Neutral Amino Acid Transporters Determine Their Retroviral Receptor Functions
Authors: Marin Mariana , Lavillette Dimitri , Kelly Sean M. , Kabat David 
Published: February 2003

ABSTRACT

A widely dispersed interference group of retroviruses that includes the feline endogenous virus (RD114), baboon endogenous virus (BaEV), human endogenous virus type W (HERV-W), and type D primate retroviruses uses the human Na
+
-dependent neutral amino acid transporter type 2 (hASCT2; gene name, SLC1A5) as a common cell surface receptor. Although hamster cells are fully resistant to these viruses and murine cells are susceptible only to BaEV and HERV-W pseudotype viruses, these rodent cells both become highly susceptible to all of the viruses after treatment with tunicamycin, an inhibitor of protein N-linked glycosylation. A partial explanation for these results was recently provided by findings that the orthologous murine transporter mASCT2 is inactive as a viral receptor, that a related (ca. 55% identity) murine paralog (mASCT1; gene name, SLC1A4) mediates infections specifically of BaEV and HERV-W, and that N-deglycosylation of mASCT1 activates it as a receptor for all viruses of this interference group. Because the only two N-linked oligosaccharides in mASCT1 occur in the carboxyl-terminal region of extracellular loop 2 (ECL2), it was inferred that this region contributes in an inhibitory manner to infections by RD114 and type D primate viruses. To directly and more thoroughly investigate the receptor active sites, we constructed and analyzed a series of hASCT2/mASCT2 chimeras and site-directed mutants. Our results suggest that a hypervariable sequence of 21 amino acids in the carboxyl-terminal portion of ECL2 plays a critical role in determining the receptor properties of ASCT2 proteins for all viruses in this interference group. In addition, we analyzed the tunicamycin-dependent viral susceptibility of hamster cells. In contrast to mASCT1, which contains two N-linked oligosaccharides that partially restrict viral infections, hamster ASCT1 contains an additional N-linked oligosaccharide clustered close to the others in the carboxyl-terminal region of ECL2. Removal of this N-linked oligosaccharide by mutagenesis enabled hamster ASCT1 to function as a receptor for all viruses of this interference group. These results strongly suggest that combinations of amino acid sequence changes and N-linked oligosaccharides in a critical carboxyl-terminal region of ECL2 control retroviral utilization of both the ASCT1 and ASCT2 receptors.