bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accuracy assessment of QuickBird stereo imagery
Authors: Noguchi Mayumi , Fraser Clive S. , Nakamura Takayuki , Shimono Takahiro , Oki Shoichi 
Published: May 2004

AbstractThe Geographical Survey Institute of Japan has recently carried out an evaluation of the metric performance of QuickBird stereo satellite imagery. This paper describes the accuracy assessment of the sensor orientation and geopositioning phases of the study, the aim of which was twofold. First, it was desired to confirm the metric potential of QuickBird imagery for 1:25 000 scale topographic mapping. Second, a determination was to be made of the accuracy attainable from the Basic image product. The techniques of rational functions and affine bundle adjustment were employed, the former with bias compensation. The results obtained both reassert the high precision of the rational functions approach and cast doubt upon the applicability of the 3D affine model for accurate geopositioning from QuickBird imagery.
Mast cells – a role in periodontal diseases?
Authors: Steinsvoll S. , Helgeland K. , Schenck K. 
Published: May 2004

AbstractObjectives:Limited attention has been given to the role mast cells may play in periodontal diseases.Background:Mast cells are indeed found abundantly below and within several types of mucosal epithelia. On the basis of their proteinase content, mast cells are divided into connective tissue (CT) and mucosal phenotypes. The CT phenotype contains both tryptase and chymase (MCTC), while the mucosal phenotype contains only tryptase (MCT). The in vivo significance of different mast cell phenotypes has not yet been fully established. Mast cells are able to phagocytose, process and present antigens as effectively as macrophages.Results:Recently mast cells were found in high numbers in chronically inflamed gingival tissue taken from patients with chronic marginal periodontitis (CMP). The number of mast cells was found to be even higher in HIV+ patients with CMP. Furthermore, mast cells also express strongly matrix metalloproteinases (MMPs), which are key enzymes in degradation of gingival extracellular matrix. Mast cells may release preformed cytokines directing local innate and adaptive immune responses. The present review will focus on possible roles for mast cells in periodontal diseases.Conclusions:We certainly feel that this is a key cell in inflamed periodontal tissue and its role in periodontitis needs to be revisited.
Analysis of a Rocking and Walking Punch—Part II: General Numerical Solution Using Quadratic Programming
Authors: Nowell D. 
Published: May 2004

AbstractThis paper pursues a numerical approach to the solution of the contact problem of a rigid punch on an incompressible half-plane, subjected to a shearing force together with a normal force which may be offset from the centerline of the punch. A piecewise-linear representation of the shear tractions is employed and quadratic programming techniques are used to solve the problem. This method enables an arbitrary load history to be followed. Results are presented which show excellent agreement with other solutions to the special cases of monotonic and steady-state cyclic loading. It is shown that the traction distribution reaches a steady-state cycle after only a few cycles of loading. The existence of an interesting stick-slip regime, where a central zone of slip is bordered by two stick regions is highlighted.
Vibration and Stability of Frictional Sliding of Two Elastic Bodies
With a Wavy Contact Interface
Authors: Nosonovsky Mikhail , Adams George G. 
Published: May 2004

Abstract
The stability of steady sliding, with Amontons-Coulomb friction, of two elastic bodies with a rough contact interface is analyzed. The bodies are modeled as elastic half-spaces, one of which has a periodic wavy surface. The steady-state solution yields a periodic set of contact and separation zones, but the stability analysis requires consideration of dynamic effects. By considering a spatial Fourier decomposition of the vibration modes, the dynamic problem is reduced to a singular integral equation for determining the eigenvectors (modes) and eigenvalues (frequencies). A pure imaginary root for an eigenvalue corresponds to a standing wave confined to the interface, while a positive/negative real part of the eigenvalue indicates instability/dissipation. A complex eigenvector indicates a complex mode of vibration. Two types of modes are considered—periodic symmetric modes with period equal to the surface waviness period and periodic antisymmetric modes with the period equal to twice the surface waviness. The singular integral equation is solved by reducing it to a system of linear algebraic equations using a Jacobi polynomial series and a collocation method. For the limit of zero friction it can be demonstrated analytically that the problem is self-adjoint and the eigenvalues, if they exist, are pure imaginary (no energy dissipation). These roots are found for a wide range of material properties and ratios of separation to contact zones lengths. For the limiting case of complete contact, the solution found corresponds to a superposition of two slip waves (generalized Rayleigh waves) traveling in opposite directions and forming a standing wave. With increasing separation zone length, the vibration frequency decreases from the slip wave frequency to the smaller surface wave frequency of the two bodies. With a nonzero separation zone, solutions can exist for material combinations which do not allow slip waves. For nonzero friction and sliding velocities, unstable solutions are found. The degree of instability is proportional to the product of the friction coefficient and the sliding velocity. These instabilities may contribute to the formation of friction-induced vibrations at high sliding speeds.
Characterization of Humanized Antibodies Secreted byAspergillus niger
Authors: Ward Michael , Lin Cherry , Victoria Doreen C. , Fox Bryan P. , Fox Judith A. , Wong David L. , Meerman Hendrik J. , Pucci Jeff P. , Fong Robin B. , Heng Meng H. , Tsurushita Naoya , Gieswein Christine , Park Minha , Wang Huaming 
Published: May 2004

ABSTRACTTwo different humanized immunoglobulin G1(κ) antibodies and an Fab′ fragment were produced byAspergillus niger. The antibodies were secreted into the culture supernatant. Both light and heavy chains were initially synthesized as fusion proteins with native glucoamylase. After antibody assembly, cleavage byA. nigerKexB protease allowed the release of free antibody. Purification by hydrophobic charge induction chromatography proved effective at removing any antibody to which glucoamylase remained attached. Glycosylation at N297 in the Fc region of the heavy chain was observed, but this site was unoccupied on approximately 50% of the heavy chains. The glycan was of the high-mannose type, with some galactose present, and the size ranged from Hex6GlcNAc2to Hex15GlcNAc2. An aglycosyl mutant form of antibody was also produced. No significant difference between the glycosylated antibody produced byAspergillusand that produced by mammalian cell cultures was observed in tests for affinity, avidity, pharmacokinetics, or antibody-dependent cellular cytotoxicity function.
Impact of Soil Drying-Rewetting Stress on Microbial Communities and Activities and on Degradation of Two Crop Protection Products
Authors: Pesaro Manuel , Nicollier Gilles , Zeyer Josef , Widmer Franco 
Published: May 2004

ABSTRACTPrior to registration of crop protection products (CPPs) their persistence in soil has to be determined under defined conditions. For this purpose, soils are collected in the field and stored for up to 3 months prior to the tests. During storage, stresses like drying may induce changes in microbiological soil characteristics (MSCs) and thus may influence CPP degradation rates. We investigated the influence of soil storage-related stress on the resistance and resilience of different MSCs by assessing the impact of a single severe drying-rewetting cycle and by monitoring recovery from this event for 34 days. The degradation and mineralization of the fungicide metalaxyl-M and the insecticide lufenuron were delayed by factors of 1.5 to 5.4 in the dried and rewetted soil compared to the degradation and mineralization in an undisturbed reference. The microbial biomass, as estimated by direct cell counting and from the soil DNA content, decreased on average by 51 and 24%, respectively. The bulk microbial activities, as determined by measuring substrate-induced respiration and fluorescein diacetate hydrolysis, increased after rewetting and recovered completely within 6 days after reequilibration. The effects onBacteria,Archaea, andPseudomonaswere investigated by performing PCR amplification of 16S rRNA genes and reverse-transcribed 16S rRNA, followed by restriction fragment length polymorphism (RFLP) and terminal RFLP (T-RFLP) fingerprinting. Statistical analyses of RFLP and T-RFLP profiles indicated that specific groups in the microbial community were sensitive to the stress. In addition, evaluation of rRNA genes and rRNA as markers for monitoring the stress responses of microbial communities revealed overall similar sensitivities. We concluded that various structural and functional MSCs were not resistant to drying-rewetting stress and that resilience depended strongly on the parameter investigated.
Cloning of the Authentic Bovine Gene Encoding Pepsinogen A and Its Expression in Microbial Cells
Authors: Muñoz Rosario , García José L. , Carrascosa Alfonso V. , Gonzalez Ramon 
Published: May 2004

ABSTRACT

Bovine pepsin is the second major proteolytic activity of rennet obtained from young calves and is the main protease when it is extracted from adult animals, and it is well recognized that the proteolytic specificity of this enzyme improves the sensory properties of cheese during maturation. Pepsin is synthesized as an inactive precursor, pepsinogen, which is autocatalytically activated at the pH of calf abomasum. A cDNA coding for bovine pepsin was assembled by fusing the cDNA fragments from two different bovine expressed sequence tag libraries to synthetic DNA sequences based on the previously described N-terminal sequence of pepsinogen. The sequence of this cDNA clearly differs from the previously described partial bovine pepsinogen sequences, which actually are rabbit pepsinogen sequences. By cloning this cDNA in different vectors we produced functional bovine pepsinogen in
Escherichia coli
and
Saccharomyces cerevisiae
. The recombinant pepsinogen is activated by low pH, and the resulting mature pepsin has milk-clotting activity. Moreover, the mature enzyme generates digestion profiles with α-, β-, or κ-casein indistinguishable from those obtained with a natural pepsin preparation. The potential applications of this recombinant enzyme include cheese making and bioactive peptide production. One remarkable advantage of the recombinant enzyme for food applications is that there is no risk of transmission of bovine spongiform encephalopathy.
A Novel Alpha-Proteobacterium Resides in the Mitochondria of Ovarian Cells of the TickIxodes ricinus
Authors: Beninati Tiziana , Lo Nathan , Sacchi Luciano , Genchi Claudio , Noda Hiroaki , Bandi Claudio 
Published: May 2004

ABSTRACTAn intracellular bacterium fromIxodes ricinusticks collected in Italy was characterized by electron microscopy (EM), PCR sequencing of the 16S rRNA gene, molecular phylogenetic analysis, and in situ hybridization (ISH). This bacterium was shown by EM to be present in the cytoplasm, as well as in the mitochondria of ovarian cells. When universal 16S rRNA bacterial primers were used, PCR amplification of ovarian DNA followed by cloning and sequencing resulted in the same sequence being found in each sample. Phylogenetic analysis of this sequence showed that the bacterium from which it was derived, tentatively designated IricES1, is part of a novel clade in the alpha subdivision of theProteobacteria. ISH and PCR assays of various tissues performed with oligonucleotides specific for the IricES1 16S rRNA showed that IricES1 is restricted to ovarian cells. Based on the results obtained, we inferred that the bacteria seen by EM in ovarian cells are a single type of bacteria, corresponding to IricES1. PCR screening of 166 ticks from various parts of Italy and one site in England showed that IricES1 was present in 96% of adult females and 44% of nymphs (unsexed). No adult males were found to be infected. Despite the apparent parasitism of host mitochondria by IricES1, the available information suggests that the bacterium has an obligate relationship with its host, although this must be confirmed.
Bacterial Community Dynamics and Hydrocarbon Degradation during a Field-Scale Evaluation of Bioremediation on a Mudflat Beach Contaminated with Buried Oil
Authors: Röling Wilfred F. M. , Milner Michael G. , Jones D. Martin , Fratepietro Francesco , Swannell Richard P. J. , Daniel Fabien , Head Ian M. 
Published: May 2004

ABSTRACT

A field-scale experiment with a complete randomized block design was performed to study the degradation of buried oil on a shoreline over a period of almost 1 year. The following four treatments were examined in three replicate blocks: two levels of fertilizer treatment of oil-treated plots, one receiving a weekly application of liquid fertilizer and the other treated with a slow-release fertilizer; and two controls, one not treated with oil and the other treated with oil but not with fertilizer. Oil degradation was monitored by measuring carbon dioxide evolution and by chemical analysis of the oil. Buried oil was degraded to a significantly greater extent in fertilized plots, but no differences in oil chemistry were observed between the two different fertilizer treatments, although carbon dioxide production was significantly higher in the oil-treated plots that were treated with slow-release fertilizer during the first 14 days of the experiment. Bacterial communities present in the beach sediments were profiled by denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA gene fragments and 16S rRNA amplified by reverse transcriptase PCR. Similarities between the DGGE profiles were calculated, and similarity matrices were subjected to statistical analysis. These analyses showed that although significant hydrocarbon degradation occurred both in plots treated with oil alone and in the plots treated with oil and liquid fertilizer, the bacterial community structure in these plots was, in general, not significantly different from that in the control plots that were not treated with oil and did not change over time. In contrast, the bacterial community structure in the plots treated with oil and slow-release fertilizer changed rapidly, and there were significant differences over time, as well as between blocks and even within plots. The differences were probably related to the higher concentrations of nutrients measured in interstitial water from the plots treated with slow-release fertilizer. Bacteria with 16S rRNA sequences closely related (>99.7% identity) to
Alcanivorax borkumensis
and
Pseudomonas stutzeri
sequences dominated during the initial phase of oil degradation in the plots treated with slow-release fertilizer. Field data were compared to the results of previous laboratory microcosm experiments, which revealed significant differences.
Response of Archaeal Communities in Beach Sediments to Spilled Oil and Bioremediation
Authors: Röling Wilfred F. M. , Couto de Brito Ivana R. , Swannell Richard P. J. , Head Ian M. 
Published: May 2004

ABSTRACT

While the contribution of
Bacteria
to bioremediation of oil-contaminated shorelines is well established, the response of
Archaea
to spilled oil and bioremediation treatments is unknown. The relationship between archaeal community structure and oil spill bioremediation was examined in laboratory microcosms and in a bioremediation field trial. 16S rRNA gene-based PCR and denaturing gradient gel analysis revealed that the archaeal community in oil-free laboratory microcosms was stable for 26 days. In contrast, in oil-polluted microcosms a dramatic decrease in the ability to detect
Archaea
was observed, and it was not possible to amplify fragments of archaeal 16S rRNA genes from samples taken from microcosms treated with oil. This was the case irrespective of whether a bioremediation treatment (addition of inorganic nutrients) was applied. Since rapid oil biodegradation occurred in nutrient-treated microcosms, we concluded that
Archaea
are unlikely to play a role in oil degradation in beach ecosystems. A clear-cut relationship between the presence of oil and the absence of
Archaea
was not apparent in the field experiment. This may have been related to continuous inoculation of beach sediments in the field with
Archaea
from seawater or invertebrates and shows that the reestablishment of
Archaea
following bioremediation cannot be used as a determinant of ecosystem recovery following bioremediation. Comparative 16S rRNA sequence analysis showed that the majority of the
Archaea
detected (94%) belonged to a novel, distinct cluster of group II uncultured
Euryarchaeota
, which exhibited less than 87% identity to previously described sequences. A minor contribution of group I uncultured
Crenarchaeota
was observed.
Automated Purification and Suspension Array Detection of 16S rRNA from Soil and Sediment Extracts by Using Tunable Surface Microparticles
Authors: Chandler Darrell P. , Jarrell Ann E. 
Published: May 2004

ABSTRACT

Autonomous, field-deployable molecular detection systems require seamless integration of complex biochemical solutions and physical or mechanical processing steps. In an attempt to simplify the fluidic requirements for integrated biodetection systems, we used tunable surface microparticles both as an rRNA affinity purification resin in a renewable microcolumn sample preparation system and as the sensor surface in a flow cytometer detector. The tunable surface detection limits in both low- and high-salt buffers were 1 ng of total RNA (∼10
4
cell equivalents) in 15-min test tube hybridizations and 10 ng of total RNA (∼10
5
cell equivalents) in hybridizations with the automated system (30-s contact time). RNA fragmentation was essential for achieving tunable surface suspension array specificity. Chaperone probes reduced but did not completely eliminate cross-hybridization, even with probes sharing <50% identity to target sequences. Nonpurified environmental extracts did not irreparably affect our ability to classify color-coded microparticles, but residual environmental constituents significantly quenched the Alexa-532 reporter fluor. Modulating surface charge did not influence the interaction of soluble environmental contaminants with conjugated beads. The automated system greatly reduced the effects of fluorescence quenching, especially in the soil background. The automated system was as efficacious as manual methods for simultaneous sample purification, hybridization, and washing prior to flow cytometry detection. The implications of unexpected target cross-hybridization and fluorescence quenching are discussed relative to the design and implementation of an integrated microbial monitoring system.
Improved Production of Heterologous Proteins by a Glucose Repression-Defective Mutant of
Kluyveromyces lactis
Authors: Donnini Claudia , Farina Francesca , Neglia Barbara , Compagno Maria Concetta , Uccelletti Daniela , Goffrini Paola , Palleschi Claudio 
Published: May 2004

ABSTRACT

The secreted production of heterologous proteins in
Kluyveromyces lactis
was studied. A glucoamylase (GAA) from the yeast
Arxula adeninivorans
was used as a reporter protein for the study of the secretion efficiencies of several wild-type and mutant strains of
K. lactis.
The expression of the reporter protein was placed under the control of the strong promoter of the glyceraldehyde-3-phosphate dehydrogenase of
Saccharomyces cerevisiae
. Among the laboratory strains tested, strain JA6 was the best producer of GAA. Since this strain is known to be highly sensitive to glucose repression and since this is an undesired trait for biomass-oriented applications, we examined heterologous protein production by using glucose repression-defective mutants isolated from this strain. One of them, a mutant carrying a
dgr151
-
1
mutation, showed a significantly improved capability of producing heterologous proteins such as GAA, human serum albumin, and human interleukin-1β compared to the parent strain.
dgr151
-
1
is an allele of
RAG5
, the gene encoding the only hexokinase present in
K. lactis
(a homologue of
S. cerevisiae HXK2
). The mutation in this strain was mapped to nucleotide position +527, resulting in a change from glycine to aspartic acid within the highly conserved kinase domain. Cells carrying the
dgr151
-
1
allele also showed a reduction in N- and O-glycosylation. Therefore, the
dgr151
strain may be a promising host for the production of heterologous proteins, especially when the hyperglycosylation of recombinant proteins must be avoided.
In Vivo Synthesis of Mammalian-Like, Hybrid-Type N-Glycans inPichia pastoris
Authors: Vervecken Wouter , Kaigorodov Vladimir , Callewaert Nico , Geysens Steven , De Vusser Kristof , Contreras Roland 
Published: May 2004

ABSTRACTThePichia pastorisN-glycosylation pathway is only partially homologous to the pathway in human cells. In the Golgi apparatus, human cells synthesize complex oligosaccharides, whereasPichiacells form mannose structures that can contain up to 40 mannose residues. This hypermannosylation of secreted glycoproteins hampers the downstream processing of heterologously expressed glycoproteins and leads to the production of protein-based therapeutic agents that are rapidly cleared from the blood because of the presence of terminal mannose residues. Here, we describe engineering of theP. pastorisN-glycosylation pathway to produce nonhyperglycosylated hybrid glycans. This was accomplished by inactivation ofOCH1and overexpression of an α-1,2-mannosidase retained in the endoplasmic reticulum andN-acetylglucosaminyltransferase I and β-1,4-galactosyltransferase retained in the Golgi apparatus. The engineered strain synthesized a nonsialylated hybrid-type N-linked oligosaccharide structure on its glycoproteins. The procedures which we developed allow glycan engineering of anyP. pastorisexpression strain and can yield up to 90% homogeneous protein-linked oligosaccharides.