bluuebunny/crossref_metadata_2025_split huggingface dataset:
Labeling Engineering Line Drawings Using Depth Reasoning
Authors: Martin R. R. , Suzuki H. , Varley P. A. C. 
Published: June 2005

AbstractAutomatic creation of B-rep models of engineering objects from freehand sketches would benefit designers. One step aims to take a line drawing (with hidden lines removed), and from it deduce an initial three-dimensional (3D) geometric realization of the visible part of the object, including junction and line labels, and depth coordinates. Most methods for producing this frontal geometry use line labeling, which takes little or no account of geometry. Thus, the line labels produced can be unreliable. Our alternative approach inflates a drawing to produce provisional depth coordinates, and from these makes deductions about line labels. Assuming many edges in the drawing are parallel to one of three main orthogonal directions, we first attempt to identify groups of parallel lines aligned with the three major axes of the object. From these, we create and solve a linear system of equations relating vertex coordinates, in the coordinate system of the major axes. We then inflate the drawing in a coordinate system based on the plane of the drawing and depth perpendicular to it. Finally, we use this geometry to identify which lines in the drawing correspond to convex, concave, or occluding edges. We discuss alternative realizations of some of the concepts, how to cope with nonisometric-projection drawings, and how to combine this approach with other labeling techniques to gain the benefits of each. We test our approach using sample drawings chosen to be representative of engineering objects. These highlight difficulties often overlooked in previous papers on line labeling. Our new approach has significant benefits.
Detail-Preserving Variational Surface Design With Multiresolution
Constraints
Authors: Boier-Martin Ioana , Ronfard Remi , Bernardini Fausto 
Published: June 2005

Abstract
We present a variational framework for rapid shape prototyping. The modeled shape is represented as a Catmull-Clark multiresolution subdivision surface which is interactively deformed by direct user input. Free-form design goals are formulated as constraints on the shape and the modeling problem is cast into a constrained optimization one. The focus of this paper is on handling multiresolution constraints of different kinds and on preserving surface details throughout the deformation process. Our approach eliminates the need for an explicit decomposition of the input model into frequency bands and the overhead associated with saving and restoring high-frequency detail after global shape fairing. Instead, we define a deformation vector field over the model and we optimize its energy. Surface details are considered as part of the rest shape and are preserved during free-form model editing. We explore approximating the solution of the optimization problem to various degrees to balance trade-offs between interactivity and accuracy of the results.
Effect of Preslaughter Events on Prevalence of
Campylobacter jejuni
and
Campylobacter coli
in Market-Weight Turkeys
Authors: Wesley Irene V. , Muraoka Wayne T. , Trampel Darrell W. , Hurd H. Scott 
Published: June 2005

ABSTRACT

The effects of events which occur prior to slaughter, such as loading, transport, and holding at an abattoir, on the prevalence of
Campylobacter
species, including
Campylobacter jejuni
and
Campylobacter coli
, were examined. Cloacal swabs from market-weight turkeys in each of five flocks were obtained on a farm prior to loading (time 1; 120 swabs per flock) and after transport and holding at the abattoir (time 2; 120 swabs per flock). A statistically significant increase in the overall prevalence of
Campylobacter
spp. was observed for cloacal swabs obtained from farm 3 following transport (
P
< 0.01). At time 2, an increase in the prevalence of
C. coli
was also noted for cloacal swabs from farms 3, 4, and 5 (
P
< 0.01). Neither the minimum time off of feed nor the distance transported from the farm to the abattoir was correlated with the increase in
C. coli
prevalence. Similarly, responses to an on-farm management questionnaire failed to detect any factors contributing to the observed changes in
Campylobacter
sp. prevalence. A SmaI macrorestriction analysis of
Campylobacter
sp. isolates recovered from flock 5 indicated that
C. coli
was more diverse than
C. jejuni
at both time 1 and time 2 (
P
< 0.01), based on a comparison of the Shannon indices of diversity and evenness.
Presence of GadD1 Glutamate Decarboxylase in Selected
Listeria monocytogenes
Strains Is Associated with an Ability To Grow at Low pH
Authors: Cotter Paul D. , Ryan Sheila , Gahan Cormac G. M. , Hill Colin 
Published: June 2005

ABSTRACT

The glutamate decarboxylase (GAD) system is critical to the survival of
Listeria monocytogenes
LO28 at low-pH stress (<pH 4.0). The GAD system classically involves two proteins, a glutamate decarboxylase enzyme coupled to a glutamate/γ-aminobutyrate antiporter, which results in the consumption of an intracellular proton for each glutamate entering the system. Uniquely among prokaryotes, some strains of
L. monocytogenes
, including strain LO28, possess genes encoding three decarboxylases (
gadD1
,
gadD2
, and
gadD3
) and two antiporters (
gadT1
and
gadT2
). These are organized in two pairs (
gadD1T1
and
gadD2T2
) and a distinct
gadD3
. While the creation of a
gadD3
mutant has not been possible, analysis of 15 isogenic mutants has confirmed previous observations that GadD2/T2 are primarily responsible for surviving severe acid challenge (pH 2.8). However, we have now established that GadD1 plays a major role in growth at mildly acidic pHs (pH 5.1). When strain variation studies revealed that a large number of
L. monocytogenes
strains (including all serotype 4 strains) lack the
gadD1
gadT1
pair, low-pH growth assays were carried out. It was found that the majority of strains that grew poorly at pH 5.1 lacked these genes. The strain-variable ability to grow in mildly acidic conditions may explain why non-serotype 4 strains of
L. monocytogenes
predominate in foods.
Cultivation System Using Glass Beads Immersed in Liquid Medium Facilitates Studies of
Streptomyces
Differentiation
Authors: Nguyen Liem D. , Kalachová Ladislava , Novotná Jana , Holub Martin , Kofroňová Olga , Benada Oldřich , Thompson Charles J. , Weiser Jaroslav 
Published: June 2005

ABSTRACT
A two-phase cultivation system was developed which will enable studies of streptomycete differentiation by molecular biological and global techniques such as transcriptomics and proteomics. The system is based on a solid phase formed by glass beads corresponding to particles in soil, clay, or sand natural habitats of streptomycetes. The beads are immersed in a liquid medium that allows easy modification or replacement of nutrients and growth factors as well as radioactive labeling of proteins. Scanning electron microscopy was used to analyze morphological differentiation of streptomycetes on glass beads and two-dimensional protein electrophoresis to demonstrate the potential of the system for analyses of protein synthesis profiles during the developmental program. This system facilitates studies of differentiation including expression and posttranslation modifications of streptomycetes proteins, secondary metabolite biosynthesis, and morphological development.
Efficacy of Various Pasteurization Time-Temperature Conditions in Combination with Homogenization on Inactivation ofMycobacterium aviumsubsp.paratuberculosisin Milk
Authors: Grant Irene R. , Williams Alan G. , Rowe Michael T. , Muir D. Donald 
Published: June 2005

ABSTRACTThe effect of various pasteurization time-temperature conditions with and without homogenization on the viability ofMycobacterium aviumsubsp.paratuberculosiswas investigated using a pilot-scale commercial high-temperature, short-time (HTST) pasteurizer and raw milk spiked with 101to 105M. aviumsubsp.paratuberculosiscells/ml. ViableM. aviumsubsp.paratuberculosiswas cultured from 27 (3.3%) of 816 pasteurized milk samples overall, 5 on Herrold's egg yolk medium and 22 by BACTEC culture. Therefore, in 96.7% of samples,M. aviumsubsp.paratuberculosishad been completely inactivated by HTST pasteurization, alone or in combination with homogenization. Heat treatments incorporating homogenization at 2,500 lb/in2, applied upstream (as a separate process) or in hold (at the start of a holding section), resulted in significantly fewer culture-positive samples than pasteurization treatments without homogenization (P< 0.001 for those in hold andP< 0.05 for those upstream). Where colony counts were obtained, the number of survivingM. aviumsubsp.paratuberculosiscells was estimated to be 10 to 20 CFU/150 ml, and the reduction in numbers achieved by HTST pasteurization with or without homogenization was estimated to be 4.0 to 5.2 log10. The impact of homogenization on clump size distribution inM. aviumsubsp.paratuberculosisbroth suspensions was subsequently assessed using a Mastersizer X spectrometer. These experiments demonstrated that large clumps ofM. aviumsubsp.paratuberculosiscells were reduced to single-cell or “miniclump” status by homogenization at 2,500 lb/in2. Consequently, when HTST pasteurization was being applied to homogenized milk, theM. aviumsubsp.paratuberculosiscells would have been present as predominantly declumped cells, which may possibly explain the greater inactivation achieved by the combination of pasteurization and homogenization.
Characterization of a Nucleus-Encoded Chitinase from the Yeast
Kluyveromyces lactis
Authors: Colussi Paul A. , Specht Charles A. , Taron Christopher H. 
Published: June 2005

ABSTRACT

Endogenous proteins secreted from
Kluyveromyces lactis
were screened for their ability to bind to or to hydrolyze chitin. This analysis resulted in identification of a nucleus-encoded extracellular chitinase (KlCts1p) with a chitinolytic activity distinct from that of the plasmid-encoded killer toxin α-subunit. Sequence analysis of cloned
KlCTS1
indicated that it encodes a 551-amino-acid chitinase having a secretion signal peptide, an amino-terminal family 18 chitinase catalytic domain, a serine-threonine-rich domain, and a carboxy-terminal type 2 chitin-binding domain. The association of purified KlCts1p with chitin is stable in the presence of high salt concentrations and pH 3 to 10 buffers; however, complete dissociation and release of fully active KlCts1p occur in 20 mM NaOH. Similarly, secreted human serum albumin harboring a carboxy-terminal fusion with the chitin-binding domain derived from KlCts1p also dissociates from chitin in 20 mM NaOH, demonstrating the domain's potential utility as an affinity tag for reversible chitin immobilization or purification of alkaliphilic or alkali-tolerant recombinant fusion proteins. Finally, haploid
K. lactis
cells harboring a
cts1
null mutation are viable but exhibit a cell separation defect, suggesting that KlCts1p is required for normal cytokinesis, probably by facilitating the degradation of septum-localized chitin.
Energy Generation from the CO Oxidation-Hydrogen Production Pathway in
Rubrivivax gelatinosus
Authors: Maness Pin-Ching , Huang Jie , Smolinski Sharon , Tek Vekalet , Vanzin Gary 
Published: June 2005

ABSTRACT

When incubated in the presence of CO gas,
Rubrivivax gelatinosus
CBS induces a CO oxidation-H
2
production pathway according to the stoichiometry CO + H
2
O → CO
2
+ H
2
. Once induced, this pathway proceeds equally well in both light and darkness. When light is not present, CO can serve as the sole carbon source, supporting cell growth anaerobically with a cell doubling time of nearly 2 days. This observation suggests that the CO oxidation reaction yields energy. Indeed, new ATP synthesis was detected in darkness following CO additions to the gas phase of the culture, in contrast to the case for a control that received an inert gas such as argon. When the CO-to-H
2
activity was determined in the presence of the electron transport uncoupler carbonyl-cyanide
m
-chlorophenylhydrazone (CCCP), the rate of H
2
production from CO oxidation was enhanced nearly 40% compared to that of the control. Upon the addition of the ATP synthase inhibitor
N
,
N
′-dicyclohexylcarbodiimide (DCCD), we observed an inhibition of H
2
production from CO oxidation which could be reversed upon the addition of CCCP. Collectively, these data strongly suggest that the CO-to-H
2
reaction yields ATP driven by a transmembrane proton gradient, but the detailed mechanism of this reaction is not yet known. These findings encourage additional research aimed at long-term H
2
production from gas streams containing CO.
Lactobacillus caseiDN-114 001 Inhibits the Ability of Adherent-InvasiveEscherichia coliIsolated from Crohn's Disease Patients To Adhere to and To Invade Intestinal Epithelial Cells
Authors: Ingrassia Isabelle , Leplingard Antony , Darfeuille-Michaud Arlette 
Published: June 2005

ABSTRACTIleal lesions in 36.4% of patients with Crohn's disease are colonized by pathogenic adherent-invasiveEscherichia coli. The aim of this study was to determine the in vitro inhibitory effects of the probiotic strain,Lactobacillus caseiDN-114 001, on adhesion to and invasion of human intestinal epithelial cells by adherent-invasiveE. coliisolated from Crohn's disease patients. The experiments were performed with undifferentiated Intestine-407 cells and with undifferentiated or differentiated Caco-2 intestinal epithelial cells. Bacterial adhesion to and invasion of intestinal epithelial cells were assessed by counting CFU. The inhibitory effects ofL. caseiwere determined after coincubation with adherent-invasiveE. colior after preincubation of intestinal cells withL. caseiprior to infection with adherent-invasiveE. coli. Inhibitory effects ofL. caseion adherent-invasiveE. coliadhesion to differentiated and undifferentiated intestinal epithelial cells reached 75% to 84% in coincubation and 43% to 62% in preincubation experiments, according to the cell lines used. Addition ofL. caseiculture supernatant to the incubation medium increasedL. caseiadhesion to intestinal epithelial cells and enhanced the inhibitory effects ofL. casei. The inhibitory effects onE. coliinvasion paralleled those on adhesion. This effect was not due to a bactericidal effect on adherent-invasiveE. colior to a cytotoxic effect on epithelial intestinal cells. AsLactobacillus caseiDN-114 001 strongly inhibits interaction of adherent-invasiveE. coliwith intestinal epithelial cells, this finding suggests that the probiotic strain could be of therapeutic value in Crohn's disease.
Versatile Use oforiCPlasmids for Functional Genomics ofMycoplasma capricolumsubsp.capricolum
Authors: Janis Carole , Lartigue Carole , Frey Joachim , Wróblewski Henri , Thiaucourt François , Blanchard Alain , Sirand-Pugnet Pascal 
Published: June 2005

ABSTRACTReplicativeoriCplasmids were recently developed for several mollicutes, including threeMycoplasmaspecies belonging to the mycoides cluster that are responsible for bovine and caprine diseases:Mycoplasma mycoidessubsp.mycoidessmall-colony type,Mycoplasma mycoidessubsp.mycoideslarge-colony type, andMycoplasma capricolumsubsp.capricolum. In this study,oriCplasmids were evaluated inM. capricolumsubsp.capricolumas genetic tools for (i) expression of heterologous proteins and (ii) gene inactivation by homologous recombination. The reporter genelacZ, encoding β-galactosidase, and the gene encoding spiralin, an abundant surface lipoprotein of the related mollicuteSpiroplasma citri, were successfully expressed. FunctionalEscherichia coliβ-galactosidase was detected in transformedMycoplasma capricolumsubsp.capricolumcells despite noticeable codon usage differences. The expression of spiralin inM. capricolumsubsp.capricolumwas assessed by colony and Western blotting. Accessibility of this protein at the cell surface and its partition into the Triton X-114 detergent phase suggest a correct maturation of the spiralin precursor. The expression of a heterologous lipoprotein in a mycoplasma raises potentially interesting applications, e.g., the use of these bacteria as live vaccines. Targeted inactivation of genelppAencoding lipoprotein A was achieved inM. capricolumsubsp.capricolumwith plasmids harboring a replication origin derived fromS. citri. Our results suggest that the selection of the infrequent events of homologous recombination could be enhanced by the use oforiCplasmids derived from related mollicute species. Mycoplasma gene inactivation opens the way to functional genomics in a group of bacteria for which a large wealth of genome data are already available and steadily growing.
Mapping of Neutralizing Epitopes on
Renibacterium salmoninarum
p57 by Use of Transposon Mutagenesis and Synthetic Peptides
Authors: Wiens Gregory D. , Owen Jennifer 
Published: June 2005

ABSTRACT

Renibacterium salmoninarum
is a gram-positive bacterium that causes bacterial kidney disease in salmonid fish. The virulence mechanisms of
R. salmoninarum
are not well understood. Production of a 57-kDa protein (p57) has been associated with isolate virulence and is a diagnostic marker for
R. salmoninarum
infection. Biological activities of p57 include binding to eukaryotic cells and immunosuppression. We previously isolated three monoclonal antibodies (4D3, 4C11, and 4H8) that neutralize p57 activity. These monoclonal antibodies (MAbs) bind to the amino-terminal region of p57 between amino acids 32 though 243; however, the precise locations of the neutralizing epitopes were not determined. Here, we use transposon mutagenesis to map the 4D3, 4C11, and 4H8 epitopes. Forty-five transposon mutants were generated and overexpressed in
Escherichia coli
BL21(DE3). The ability of MAbs 4D3, 4H8, and 4C11 to bind each mutant protein was assessed by immunoblotting. Transposons inserting between amino acids 51 and 112 disrupted the 4H8 epitope. Insertions between residues 78 and 210 disrupted the 4C11 epitope, while insertions between amino acids 158 and 234 disrupted the 4D3 epitope. The three MAbs failed to bind overlapping, 15-mer peptides spanning these regions, suggesting that the epitopes are discontinuous in conformation. We conclude that recognition of secondary structure on the amino terminus of p57 is important for neutralization. The epitope mapping studies suggest directions for improvement of MAb-based immunoassays for detection of
R. salmoninarum
-infected fish.
Cloning and Characterization of the Glucosidase II Alpha Subunit Gene of
Trichoderma reesei
: a Frameshift Mutation Results in the Aberrant Glycosylation Profile of the Hypercellulolytic Strain Rut-C30
Authors: Geysens Steven , Pakula Tiina , Uusitalo Jaana , Dewerte Isabelle , Penttilä Merja , Contreras Roland 
Published: June 2005

ABSTRACT

We describe isolation and characterization of the gene encoding the glucosidase II alpha subunit (GIIα) of the industrially important fungus
Trichoderma reesei
. This subunit is the catalytic part of the glucosidase II heterodimeric enzyme involved in the structural modification within the endoplasmic reticulum (ER) of N-linked oligosaccharides present on glycoproteins. The gene encoding GIIα (
gls2
α) in the hypercellulolytic strain Rut-C30 contains a frameshift mutation resulting in a truncated gene product. Based on the peculiar monoglucosylated N-glycan pattern on proteins produced by the strain, we concluded that the truncated protein can still hydrolyze the first α-1,3-linked glucose residue but not the innermost α-1,3-linked glucose residue from the Glc
2
Man
9
GlcNAc
2
N-glycan ER structure. Transformation of the Rut-C30 strain with a repaired
T. reesei gls2
α gene changed the glycosylation profile significantly, decreasing the amount of monoglucosylated structures and increasing the amount of high-mannose N-glycans. Full conversion to high-mannose carbohydrates was not obtained, and this was probably due to competition between the endogenous mutant subunit and the introduced wild-type GIIα protein. Since glucosidase II is also involved in the ER quality control of nascent polypeptide chains, its transcriptional regulation was studied in a strain producing recombinant tissue plasminogen activator (tPA) and in cultures treated with the stress agents dithiothreitol (DTT) and brefeldin A (BFA), which are known to block protein transport and to induce the unfolded protein response. While the mRNA levels were clearly upregulated upon tPA production or BFA treatment, no such enhancement was observed after DTT addition.
Accelerated Sulfur Cycle in Coastal Marine Sediment beneath Areas of Intensive Shellfish Aquaculture
Authors: Asami Hiroki , Aida Masato , Watanabe Kazuya 
Published: June 2005

ABSTRACT

Prokaryotes in marine sediments taken from two neighboring semienclosed bays (the Yamada and Kamaishi bays) at the Sanriku coast in Japan were investigated by the culture-independent molecular phylogenetic approach coupled with chemical and activity analyses. These two bays were chosen in terms of their similar hydrogeological and chemical characteristics but different usage modes; the Yamada bay has been used for intensive shellfish aquaculture, while the Kamaishi bay has a commercial port and is not used for aquaculture. Substantial differences were found in the phylogenetic composition of 16S rRNA gene clone libraries constructed for the Yamada and Kamaishi sediments. In the Yamada library, phylotypes affiliated with δ
-Proteobacteria
were the most abundant, and those affiliated with γ
-Proteobacteria
were the second-most abundant. In contrast, the Kamaishi library was occupied by phylotypes affiliated with
Planctomycetes
, γ
-Proteobacteria
, δ
-Proteobacteria
, and
Crenarchaeota
. In the γ
-Proteobacteria
, many Yamada phylotypes were related to free-living and symbiotic sulfur oxidizers, whereas the Kamaishi phylotype was related to the genus
Pseudomonas
. These results allowed us to hypothesize that sulfate-reducing and sulfur-oxidizing bacteria have become abundant in the Yamada sediment. This hypothesis was supported by quantitative competitive PCR (qcPCR) with group-specific primers. The qcPCR also suggested that organisms closely related to
Desulfotalea
in the
Desulfobulbaceae
were the major sulfate-reducing bacteria in these sediments. In addition, potential sulfate reduction and sulfur oxidation rates in the sediment samples were determined, indicating that the sulfur cycle has become active in the Yamada sediment beneath the areas of intensive shellfish aquaculture.
FLO11-Based Model for Air-Liquid Interfacial Biofilm Formation bySaccharomyces cerevisiae
Authors: Zara Severino , Bakalinsky Alan T. , Zara Giacomo , Pirino Giorgia , Demontis Maria Antonietta , Budroni Marilena 
Published: June 2005

ABSTRACTSardinian wine strains ofSaccharomyces cerevisiaeused to make sherry-like wines form a biofilm at the air-liquid interface at the end of ethanolic fermentation, when grape sugar is depleted and further growth becomes dependent on access to oxygen. Here, we show thatFLO11, which encodes a hydrophobic cell wall glycoprotein, is required for the air-liquid interfacial biofilm and that biofilm cells have a buoyant density greater than the suspending medium. We propose a model for biofilm formation based on an increase in cell surface hydrophobicity occurring at the diauxic shift. This increase leads to formation of multicellular aggregates that effectively entrap carbon dioxide, providing buoyancy. A visible biofilm appears when a sufficient number of hydrophobic cell aggregates are carried to and grow on the liquid surface.