bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbiological and clinical outcomes and patient satisfaction for two treatment options in the edentulous lower jaw after 10 years of function
Authors: Quirynen Marc , Alsaadi Ghada , Pauwels Martine , Haffajee Anne , Van Steenberghe Daniel , Naert Ignace 
Published: May 2005

AbstractBackground: Long‐term data on microbiological and clinical outcome as well as on patient satisfaction after implant therapy in the edentulous mandible are limited. Especially comparisons between fixed full prostheses (FFPs) and overdentures (ODs), or between anchoring systems for the latter are scarce.Aim: This study aimed to evaluate both of these parameters at the 10‐year follow‐up in a group of fully edentulous patients rehabilitated via an OD or a FFP (the latter to allow inter‐group comparison).Material and methods: A total of 37 fully edentulous patients (25 ODs, 12 FFPs, age at implant installation ranged from 36 to 85 years) participated in this study. All subjects received their implants (Brånemark System®, Nobel Biocare AB, Gothenburg, Sweden) 10 years previously. For the ODs different attachment systems (bar, magnets, ball) had been applied that allowed a further intra‐group comparison. At the follow‐up visit, 10 years after the abutment insertion, a series of periodontal parameters were recorded, long‐cone radiographs were taken and subgingival plaque samples were collected for analysis using checkerboard DNA–DNA hybridization. The clinical and radiographic data were recorded at abutment connection and after 1 and 10 years.Results: After 10 years of loading, mean plaque and bleeding indices and changes in attachment or marginal bone level were not significantly different, neither between the OD and FFP group, nor within the OD group. The marginal bone loss between abutment connection and year 10 was 0.86 and 0.73 mm for OD and FFP groups, respectively. The subgingival microbiota at implant sites from all (sub)‐groups was comparable, with low numbers of DNA counts (±10 × 105) but high detection frequencies of Actinobacillus actinomycetemcomitans (>90%), Porphyromonas gingivalis (>85%) and Tannerella forsythensis (30%). The composition of the subgingival microbiota was influenced by probing depth and bleeding tendency. Patient satisfaction was very high for both types of prosthetic rehabilitation. The FFP group scored only slightly better for chewing comfort and general satisfaction.Conclusion: These data indicate that from the clinical and microbiological standpoint, as well as patient satisfaction, both an OD and a FFP offer a favourable long‐term outcome.
Measured Adiabatic Effectiveness and Heat Transfer for Blowing From
the Tip of a Turbine Blade
Authors: Christophel J. R. , Couch E. , Thole K. A. , Cunha F. J. 
Published: May 2005

Abstract
The clearance gap between the tip of a turbine blade and the shroud has an inherent leakage flow from the pressure side to the suction side of the blade. This leakage flow of combustion gas and air mixtures leads to severe heat transfer rates on the blade tip of the high-pressure turbine. As the thermal load to the blade increases, blade alloy oxidation and erosion rates increase thereby adversely affecting component life. The subject of this paper is the cooling effectiveness levels and heat transfer coefficients that result from blowing through two holes placed in the forward region of a blade tip. These holes are referred to as dirt purge holes and are generally required for manufacturing purposes and expelling dirt from the coolant flow when operating in sandy environments. Experiments were performed in a linear blade cascade for two tip-gap heights over a range of blowing ratios. Results indicated that the cooling effectiveness was highly dependent on the tip-gap clearance with better cooling achieved at smaller clearances. Also, heat transfer was found to increase with blowing. In considering an overall benefit of cooling from the dirt purge blowing, a large benefit was realized for a smaller tip gap as compared with a larger tip gap.
Cooling the Tip of a Turbine Blade Using Pressure Side Holes—Part I:
Adiabatic Effectiveness Measurements
Authors: Christophel J. R. , Thole K. A. , Cunha F. J. 
Published: May 2005

Abstract
Durability of turbine blade tips has been and continues to be challenging, particularly since increasing turbine inlet temperatures is the driver for improving turbine engine performance. As a result, cooling methods along the blade tip are crucial. Film-cooling is one typically used cooling method whereby coolant is supplied through holes placed along the pressure side of a blade. The subject of this paper is to evaluate the adiabatic effectiveness levels that occur on the blade tip through blowing coolant from holes placed near the tip of a blade along the pressure side. A range of blowing ratios was studied whereby coolant was injected from holes placed along the pressure side tip of a large-scale blade model. Also present were dirt purge holes on the blade tip, which is part of a commonly used blade design to expel any large particles present in the coolant stream. Experiments were conducted in a linear cascade with a scaled-up turbine blade whereby the Reynolds number of the engine was matched. This paper, which is Part 1 of a two part series, compares adiabatic effectiveness levels measured along a blade tip, while Part 2 combines measured heat transfer coefficients with the adiabatic effectiveness levels to assess the overall cooling benefit of pressure side blowing near a blade tip. The results show much better cooling can be achieved for a small tip gap compared with a large tip gap with different flow phenomena occurring for each tip gap setting.
Efficient Parallel Simulation of Direct Methanol Fuel Cell
Models
Authors: Rajasekaran S. , Ammar R. , Reifsnider K. , Achenie L. , Mohamed A. , Zhang G. , Ahmed M. 
Published: May 2005

Abstract
Fuel cells, as highly efficient and environment-friendly power sources, have attracted ever-increasing research and development in the past few decades. Mathematical modeling and simulation are applied to examine the influence of the different physical and electrochemical phenomena occurring in the structure of the fuel cell during operation. Such simulation programs take a very long time (of the order of days or even weeks) to run, especially when accurate results are called for. To achieve accurate results and more insight, we need even more complex models (two- and three-dimensional models). In this paper, we present techniques for the parallel simulation of a mathematical model of direct methanol fuel cells (DMFC). In particular, we employ a paradigm called LessTalk. LessTalk is a general technique that can be employed to reduce communications in parallel computations. Using LessTalk, we have achieved almost linear speedup in simulating the DMFC model. The results were validated against measurements available from the Connecticut Global Fuel Cell Center (CGFCC).
High Frequency Surface Heat Flux Imaging of Bypass
Transition
Authors: Anthony Richard J. , Jones Terry V. , LaGraff John E. 
Published: May 2005

Abstract
A high-frequency surface heat flux imaging technique was used to investigate bypass transition induced by freestream turbulence. Fundamental experiments were carried out at the University of Oxford using high-density thin film arrays on a flat plate wind tunnel model. Bypass transition was induced by grid-generated turbulence with varying intensities of 2.3%, 4.2%, and 17% with a fixed integral length scale of approximately 12mm. Unique high resolution temporal heat flux images are shown which detail significant differences between unsteady surface heat flux events induced by freestream turbulence and the classical Emmons-type spots which many turbomachinery transition models are based on. The temporal imaging technique presented allows study of unsteady surface heat transfer in detail, and helps elucidate the complex nature of transition in the high-disturbance environment of turbomachinery.
Flow and Heat Transfer in an Internally Ribbed Duct With Rotation: An
Assessment of Large Eddy Simulations and Unsteady Reynolds-Averaged
Navier-Stokes Simulations
Authors: Saha A. K. , Acharya Sumanta 
Published: May 2005

Abstract
Large eddy simulations (LES) and unsteady Reynolds averaged Navier-Stokes (URANS) simulations have been performed for flow and heat transfer in a rotating ribbed duct. The ribs are oriented normal to the flow and arranged in a staggered configuration on the leading and trailing surfaces. The LES results are based on a higher-order accurate finite difference scheme with a dynamic Smagorinsky model for the subgrid stresses. The URANS procedure utilizes a two equation k-ε model for the turbulent stresses. Both Coriolis and centrifugal buoyancy effects are included in the simulations. The URANS computations have been carried out for a wide range of Reynolds number (Re=12,500-100,000), rotation number (Ro=0-0.5) and density ratio (Δρ∕ρ=0-0.5), while LES results are reported for a single Reynolds number of 12,500 without and with rotation (Ro=0.12,Δρ∕ρ=0.13). Comparison is made between the LES and URANS results, and the effects of various parameters on the flow field and surface heat transfer are explored. The LES results clearly reflect the importance of coherent structures in the flow, and the unsteady dynamics associated with these structures. The heat transfer results from both LES and URANS are found to be in reasonable agreement with measurements. LES is found to give higher heat transfer predictions (5–10% higher) than URANS. The Nusselt number ratio (Nu∕Nu0) is found to decrease with increasing Reynolds number on all walls, while they increase with the density ratio along the leading and trailing walls. The Nusselt number ratio on the trailing and sidewalls also increases with rotation. However, the leading wall Nusselt number ratio shows an initial decrease with rotation (till Ro=0.12) due to the stabilizing effect of rotation on the leading wall. However, beyond Ro=0.12, the Nusselt number ratio increases with rotation due to the importance of centrifugal-buoyancy at high rotation.
Strain-Modulated Adatom and Surface Vacancy Pair
Interactions
Authors: Liu P. , Kukta R. V. , Kouris D. 
Published: May 2005

Abstract
Adsorbed atoms (adatoms) and vacancies have a significant role to play in the physics of surfaces and the mechanisms of film growth on a substrate. This paper investigates the effect of applied or residual strain on the energetic interaction between pairs of adatoms and vacancies. The analysis is based on a continuum-level point-defect model, where adatoms and vacancies have strain-dependent properties. Atomistic calculations are used to evaluate the defect properties for Si(111). The result is used as input for the defect model in order to investigate the strength and character of the interaction versus strain, separation distance, and relative orientation of the defects. It is found that strain may cause the defects to align in certain direction and modulate their interaction between repulsion and attraction, providing a mechanism for controlled building of nanostructures.
Relationship of
DFG16
to the Rim101p pH Response Pathway in
Saccharomyces cerevisiae
and
Candida albicans
Authors: Barwell Karen J. , Boysen Jacob H. , Xu Wenjie , Mitchell Aaron P. 
Published: May 2005

ABSTRACT

Many fungal pH responses depend upon conserved Rim101p/PacC transcription factors, which are activated by C-terminal proteolytic processing. The means by which environmental pH is sensed by this pathway are not known. Here, we report a screen of the
Saccharomyces cerevisiae
viable deletion mutant library that has yielded a new gene required for processed Rim101p accumulation,
DFG16.
An
S. cerevisiae dfg16
Δ mutant expresses Rim101p-repressed genes at elevated levels. In addition,
Candida albicans dfg16
Δ/
dfg16Δ
mutants are defective in alkaline pH-induced filamentation, and their defect is suppressed by expression of truncated Rim101-405p. Thus, Dfg16p is a functionally conserved Rim101p pathway member. Many proteins required for processed Rim101p accumulation are members of the ESCRT complex, which functions in the formation of multivesicular bodies (MVBs). Staining with the dye FM4-64 indicates that the
S. cerevisiae dfg16
Δ mutant does not have an MVB defect. We find that two transcripts,
PRY1
and
ASN1
, respond to mutations that affect both the Rim101p and MVB pathways but not to mutations that affect only one pathway. The
S. cerevisiae dfg16
Δ mutation does not affect
PRY1
and
ASN1
expression, thus confirming that Dfg16p function is restricted to the Rim101p pathway. Dfg16p is homologous to
Aspergillus nidulans
PalH, a component of the well-characterized PacC processing pathway. We verify that the previously recognized PalH homolog, Rim21p, also functions in the
S. cerevisiae
Rim101p pathway. Dfg16p is predicted to have seven membrane-spanning segments and a long hydrophilic C-terminal region, as expected if Dfg16p were a G-protein-coupled receptor.
Molecular and Functional Analyses of
poi-2
, a Novel Gene Highly Expressed in Sexual and Perithecial Tissues of
Neurospora crassa
Authors: Kim Hyojeong , Nelson Mary Anne 
Published: May 2005

ABSTRACT

The
poi-2
gene is highly and specifically expressed in starved and sexual tissues of the filamentous fungus
Neurospora crassa
. It encodes a 27-kDa protein, as shown by in vitro transcription and translation. The POI2 protein contains a hydrophobic signal sequence at the amino terminus followed by novel 16 tandem repeats of 13 to 14 amino acid residues; all repeats are separated by Kex2 processing sites. Repeat-induced point mutation (RIP)-mediated gene disruption was used to generate
poi-2
mutants, and the mutated sequences showed either one of two distinct patterns: typical RIPs (GC-to-AT transitions) or insertion-deletion (indel) mutations. Although the
poi-2
strains contained numerous mutations, all retained intact open reading frames (ORFs) of various lengths. They showed greatly reduced vegetative growth and protoperithecial formation and low viability of their sexual progeny. All
poi-2
mutants had similar defects in male fertility and the mating response, but the nature of female fertility defects varied and corresponded to the length of the residual
poi-2
ORF. Mutants with ORFs of approximately normal length occasionally completed sexual development and produced viable ascospores, while a mutant with a severely truncated ORF was female sterile due to its inability to form protoperithecia. Thus,
poi-2
is essential for differentiation of female reproductive structures and perithecial development as well as for normal vegetative growth. The POI2 protein is involved in the mating response, probably as a component in the pathway rather than as a pheromone.
Protein Engineering of the Archetypal Nitroarene Dioxygenase of
Ralstonia
sp. Strain U2 for Activity on Aminonitrotoluenes and Dinitrotoluenes through Alpha-Subunit Residues Leucine 225, Phenylalanine 350, and Glycine 407
Authors: Keenan Brendan G. , Leungsakul Thammajun , Smets Barth F. , Mori Masa-aki , Henderson David E. , Wood Thomas K. 
Published: May 2005

ABSTRACT

Naphthalene dioxygenase (NDO) from
Ralstonia
sp. strain U2 has not been reported to oxidize nitroaromatic compounds. Here, saturation mutagenesis of NDO at position F350 of the α-subunit (NagAc) created variant F350T that produced 3-methyl-4-nitrocatechol from 2,6-dinitrotoluene (26DNT), that released nitrite from 23DNT sixfold faster than wild-type NDO, and that produced 3-amino-4-methyl-5-nitrocatechol and 2-amino-4,6-dinitrobenzyl alcohol from 2-amino-4,6-dinitrotoluene (2A46DNT) (wild-type NDO has no detectable activity on 26DNT and 2A46DNT). DNA shuffling identified the beneficial NagAc mutation G407S, which when combined with the F350T substitution, increased the rate of NDO oxidation of 26DNT, 23DNT, and 2A46DNT threefold relative to variant F350T. DNA shuffling of NDO
nagAcAd
also generated the NagAc variant G50S/L225R/A269T with an increased rate of 4-amino-2-nitrotoluene (4A2NT; reduction product of 2,4-dinitrotoluene) oxidation; from 4A2NT, this variant produced both the previously uncharacterized oxidation product 4-amino-2-nitrocresol (enhanced 11-fold relative to wild-type NDO) as well as 4-amino-2-nitrobenzyl alcohol (4A2NBA; wild-type NDO does not generate this product). G50S/L225R/A269T also had increased nitrite release from 23DNT (14-fold relative to wild-type NDO) and generated 2,3-dinitrobenzyl alcohol (23DNBA) fourfold relative to wild-type NDO. The importance of position L225 for catalysis was confirmed through saturation mutagenesis; relative to wild-type NDO, NDO variant L225R had 12-fold faster generation of 4-amino-2-nitrocresol and production of 4A2NBA from 4A2NT as well as 24-fold faster generation of nitrite and 15-fold faster generation of 23DNBA from 23DNT. Hence, random mutagenesis discovered two new residues, G407 and L225, that influence the regiospecificity of Rieske non-heme-iron dioxygenases.
Mosaic Prophages with Horizontally Acquired Genes Account for the Emergence and Diversification of the Globally Disseminated M1T1 Clone of
Streptococcus pyogenes
Authors: Aziz Ramy K. , Edwards Robert A. , Taylor William W. , Low Donald E. , McGeer Allison , Kotb Malak 
Published: May 2005

ABSTRACT
The recrudescence of severe invasive group A streptococcal (GAS) diseases has been associated with relatively few strains, including the M1T1 subclone that has shown an unprecedented global spread and prevalence and high virulence in susceptible hosts. To understand its unusual epidemiology, we aimed to identify unique genomic features that differentiate it from the fully sequenced M1 SF370 strain. We constructed DNA microarrays from an M1T1 shotgun library and, using differential hybridization, we found that both M1 strains are 95% identical and that the 5% unique M1T1 clone sequences more closely resemble sequences found in the M3 strain, which is also associated with severe disease. Careful analysis of these unique sequences revealed three unique prophages that we named M1T1.X, M1T1.Y, and M1T1.Z. While M1T1.Y is similar to phage 370.3 of the M1-SF370 strain, M1T1.X and M1T1.Z are novel and encode the toxins SpeA2 and Sda1, respectively. The genomes of these prophages are highly mosaic, with different segments being related to distinct streptococcal phages, suggesting that GAS phages continue to exchange genetic material. Bioinformatic and phylogenetic analyses revealed a highly conserved open reading frame (ORF) adjacent to the toxins in 18 of the 21 toxin-carrying GAS prophages. We named this ORF paratox, determined its allelic distribution among different phages, and found linkage disequilibrium between particular paratox alleles and specific toxin genes, suggesting that they may move as a single cassette. Based on the conservation of paratox and other genes flanking the toxins, we propose a recombination-based model for toxin dissemination among prophages. We also provide evidence that a minor population of the M1T1 clonal isolates have exchanged their virulence module on phage M1T1.Y, replacing it with a different module identical to that found on a related M3 phage. Taken together, the data demonstrate that mosaicism of the GAS prophages has contributed to the emergence and diversification of the M1T1 subclone.
Persistence ofStreptococcus pyogenesin Stationary-Phase Cultures
Authors: Wood Daniel N. , Chaussee Michelle A. , Chaussee Michael S. , Buttaro Bettina A. 
Published: May 2005

ABSTRACTIn addition to causing fulminant disease,Streptococcus pyogenesmay be asymptomatically carried between recurrent episodes of pharyngitis. To better understand streptococcal carriage, we characterized in vitro long-term stationary-phase survival (>4 weeks) ofS. pyogenes. When grown in sugar-limited Todd-Hewitt broth,S. pyogenescells remained culturable for more than 1 year. Both Todd-Hewitt supplemented with excess glucose and chemically defined medium allowed survival for less than 1 week. After 4 weeks of survival in sugar-limited Todd-Hewitt broth, at least 103CFU per ml remained. When stained with fluorescent live-dead viability stain, there were a number of cells with intact membranes that were nonculturable. Under conditions that did not support persistence, these cells disappeared 2 weeks after loss of culturability. In persistent cultures, these may be cells that are dying during cell turnover. After more than 4 weeks in stationary phase, the culturable cells formed two alternative colony phenotypes: atypical large colonies and microcolonies. Protein expression in two independently isolated microcolony strains, from 14-week cultures, was examined by use of two-dimensional electrophoresis. The proteomes of these two strains exhibited extensive changes compared to the parental strain. While some of these changes were common to the two strains, many of the changes were unique to a single strain. Some of the common changes were in metabolic pathways, suggesting a possible alternate metabolism for the persisters. Overall, these data suggest that under certain in vitro conditions,S. pyogenescells can persist for greater than 1 year as a dynamic population.
Transcription Activation In Vitro by the
Bradyrhizobium japonicum
Regulatory Protein FixK
2
Authors: Mesa Socorro , Ucurum Zöhre , Hennecke Hauke , Fischer Hans-Martin 
Published: May 2005

ABSTRACT

In
Bradyrhizobium japonicum
, the N
2
-fixing root nodule endosymbiont of soybean, a group of genes required for microaerobic, anaerobic, or symbiotic growth is controlled by FixK
2
, a key regulator that is part of the FixLJ-FixK
2
cascade. FixK
2
belongs to the family of cyclic AMP receptor protein/fumarate and nitrate reductase (CRP/FNR) transcription factors that recognize a palindromic DNA motif (CRP/FNR box) associated with the regulated promoters. Here, we report on a biochemical analysis of FixK
2
and its transcription activation activity in vitro. FixK
2
was expressed in
Escherichia coli
and purified as a soluble N-terminally histidine-tagged protein. Gel filtration experiments revealed that increasing the protein concentration shifts the monomer-dimer equilibrium toward the dimer. Purified FixK
2
productively interacted with the
B. japonicum
σ
80
-RNA polymerase holoenzyme, but not with
E. coli
σ
70
-RNA polymerase holoenzyme, to activate transcription from the
B. japonicum fixNOQP
,
fixGHIS
, and
hemN
2
promoters in vitro. Furthermore, FixK
2
activated transcription from the
E. coli
FF(−41.5) model promoter, again only in concert with
B. japonicum
RNA polymerase. All of these promoters are so-called class II CRP/FNR-type promoters. We showed by specific mutagenesis that the FixK
2
box at nucleotide position −40.5 in the
hemN
2
promoter, but not that at −78.5, is crucial for activation both in vivo and in vitro, which argues against recognition of a potential class III promoter. Given the lack of any evidence for the presence of a cofactor in purified FixK
2
, we surmise that FixK
2
alone is sufficient to activate in vitro transcription to at least a basal level. This contrasts with all well-studied CRP/FNR-type proteins, which do require coregulators.