bluuebunny/crossref_metadata_2025 huggingface dataset:
A Simple Local Sensitivity Analysis Tool for Nonignorable Coarsening: Application to Dependent Censoring
Authors: Zhang Jiameng , Heitjan Daniel F.
Published: June 2006

Summary Right‐ and interval‐censored data are common special cases of coarsened data (Heitjan and Rubin, 1991, Annals of Statistics19, 2244–2253). As with missing data, standard statistical methods that ignore the random nature of the coarsening mechanism may lead to incorrect inferences. We extend a simple sensitivity analysis tool, the index of local sensitivity to nonignorability (Troxel, Ma, and Heitjan, 2004, Statistica Sinica14, 1221–1237), to the evaluation of nonignorability of the coarsening process in the general coarse‐data model. By converting this index into a simple graphical display one can easily assess the sensitivity of key inferences to nonignorable coarsening. We illustrate the validity of the method with a simulated example, and apply it to right‐censored data from an observational study of cardiac transplantation and to interval‐censored data on time to detectable viral load from a clinical trial in HIV disease.
Case‐Cohort Designs and Analysis for Clustered Failure Time Data
Authors: Lu Shou‐En , Shih Joanna H.
Published: June 2006

SummaryCase‐cohort design is an efficient and economical design to study risk factors for infrequent disease in a large cohort. It involves the collection of covariate data from all failures ascertained throughout the entire cohort, and from the members of a random subcohort selected at the onset of follow‐up. In the literature, the case‐cohort design has been extensively studied, but was exclusively considered for univariate failure time data. In this article, we propose case‐cohort designs adapted to multivariate failure time data. An estimation procedure with the independence working model approach is used to estimate the regression parameters in the marginal proportional hazards model, where the correlation structure between individuals within a cluster is left unspecified. Statistical properties of the proposed estimators are developed. The performance of the proposed estimators and comparisons of statistical efficiencies are investigated with simulation studies. A data example from the Translating Research into Action for Diabetes (TRIAD) study is used to illustrate the proposed methodology.
Interval Mapping of Quantitative Trait Loci for Time‐to‐Event Data with the Proportional Hazards Mixture Cure Model
Authors: Liu Mengling , Lu Wenbin , Shao Yongzhao
Published: June 2006

SummaryInterval mapping using normal mixture models has been an important tool for analyzing quantitative traits in experimental organisms. When the primary phenotype is time‐to‐event, it is natural to use survival models such as Cox's proportional hazards model instead of normal mixtures to model the phenotype distribution. An extra challenge for modeling time‐to‐event data is that the underlying population may consist of susceptible and nonsusceptible subjects. In this article, we propose a semiparametric proportional hazards mixture cure model which allows missing covariates. We discuss applications to quantitative trait loci (QTL) mapping when the primary trait is time‐to‐event from a population of mixed susceptibility. This model can be used to characterize QTL effects on both susceptibility and time‐to‐event distribution, and to estimate QTL location. The model can naturally incorporate covariate effects of other risk factors. Maximum likelihood estimates for the parameters in the model as well as their corresponding variance estimates can be obtained numerically using an EM‐type algorithm. The proposed methods are assessed by simulations under practical settings and illustrated using a real data set containing survival times of mice after infection withListeria monocytogenes. An extension to multiple intervals is also discussed.
Statistical Inference in a Stochastic Epidemic SEIR Model with Control Intervention: Ebola as a Case Study
Authors: Lekone Phenyo E. , Finkenstädt Bärbel F.
Published: June 2006

SummaryA stochastic discrete‐time susceptible‐exposed‐infectious‐recovered (SEIR) model for infectious diseases is developed with the aim of estimating parameters from daily incidence and mortality time series for an outbreak of Ebola in the Democratic Republic of Congo in 1995. The incidence time series exhibit many low integers as well as zero counts requiring an intrinsically stochastic modeling approach. In order to capture the stochastic nature of the transitions between the compartmental populations in such a model we specify appropriate conditional binomial distributions. In addition, a relatively simple temporally varying transmission rate function is introduced that allows for the effect of control interventions. We develop Markov chain Monte Carlo methods for inference that are used to explore the posterior distribution of the parameters. The algorithm is further extended to integrate numerically over state variables of the model, which are unobserved. This provides a realistic stochastic model that can be used by epidemiologists to study the dynamics of the disease and the effect of control interventions.
A Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification
Authors: Yuan Ming , Kendziorski Christina
Published: June 2006

SummaryAlthough both clustering and identification of differentially expressed genes are equally essential in most microarray studies, the two tasks are often conducted without regard to each other. This is clearly not the most efficient way of extracting information. The main aim of this article is to develop a coherent statistical method that can simultaneously cluster and detect differentially expressed genes. Through information sharing between the two tasks, the proposed approach gives more sensible clustering among genes and is more sensitive in identifying differentially expressed genes. The improvement over existing methods is illustrated in both our simulation results and a case study.
A Semiparametric Empirical Likelihood Method for Biased Sampling Schemes with Auxiliary Covariates
Authors: Wang Xiaofei , Zhou Haibo
Published: June 2006

SummaryWe consider a semiparametric inference procedure for data from epidemiologic studies conducted with a two‐component sampling scheme where both a simple random sample and multiple outcome‐ or outcome‐/auxiliary‐dependent samples are observed. This sampling scheme allows the investigators to oversample certain subpopulations believed to have more information about the regression model while still gaining insights about the underlying population through the simple random sample. We focus on settings where there is no additional information about the parent cohort and the sampling probability is nonidentifiable. We motivate our problem with an ongoing study to assess the association between the mutation level of epidermal growth factor receptor (EGFR) and the antitumor response to EGFR‐targeted therapy among nonsmall cell lung cancer patients. The proposed method applies to both binary and multicategorical outcome data and allows an arbitrary link function in the framework of generalized linear models. Simulation studies show that the proposed estimator has nice small sample properties. The proposed method is illustrated with a data example.
Fragment Length Distributions and Collision Probabilities for AFLP Markers
Authors: Gort Gerrit , Koopman Wim J. M. , Stein Alfred
Published: June 2006

Summary AFLP is a DNA fingerprinting technique frequently used in plant and animal sciences. A drawback of the technique is the occurrence of multiple DNA fragments of the same length in a single AFLP lane, which we name a collision. In this article we quantify the problem. The well‐known birthday problem plays a role. Calculation of collision probabilities requires a fragment length distribution (fld). We discuss three ways to estimate the fld: based on theoretical considerations, on in‐silico determination using DNA sequence data from Arabidopsis thaliana, or on direct estimation from AFLP data. In the latter case we use a generalized linear model with monotone smoothing of the fragment length probabilities. Collision probabilities are calculated from two perspectives, assuming known fragment counts and assuming known band counts. We compare results for a number of fld's, ranging from uniform to highly skewed. The conclusion is that collisions occur often, with higher probabilities for higher numbers of bands, for more skewed distributions, and, to a lesser extent, for smaller scoring ranges. For a typical plant genome an AFLP with 19 bands is likely to contain the first collision. Practical implications of collisions are discussed. AFLP examples from lettuce and chicory are used for illustration.
Property rights, production technology, and deforestation: cocoa in Cameroon
Authors: Kazianga Harounan , Masters William A.
Published: June 2006

In this article, we use a vintage‐capital model with risk of eviction to assess cocoa farmers' response to changes in their tenure security and to the introduction of a new, faster‐maturing cocoa variety. The model is calibrated with data from Cameroon in calendar year 2000, and then used to simulate the effects of institutional and technical change on farmer welfare and deforestation rates. Our findings can be summarized in three points. First, improved tenure security over cocoa fields increases farmers' consumption and welfare, but at the expense of more deforestation. Second, the introduction of new cocoa varieties with faster maturity and higher input response also unambiguously raises farmers' consumption and welfare. Doing so increases deforestation under insecure land tenure, but slows down deforestation under secure land tenure. Third, when introducing the two innovations together (more security and also new varieties), there is both an increase in welfare and a decline in deforestation. In sum, the availability of new cocoa cultivars calls for stronger tenure security, to accommodate investment in the new technology without increasing deforestation.
Strategic pricing in a differentiated product oligopoly model: fluid milk in Boston
Authors: Canan Basak , Cotterill Ronald W.
Published: June 2006

In an imperfectly competitive industry, differentiated products compete with each other with price rather than quantity as the strategic variable. Several previous studies have employed a generalized Nash–Bertrand model: Liang (1989), Cotterill (1994), Cotterill et al. (2000), and Kinoshita et al. (2002); however, only Liang has explored the theoretical foundations of that model. This article generalizes the Liang two‐good model to three goods. A surprising and important result follows. Price‐conjectural variations do not exist in models with three or more goods. Price‐reaction functions, however, exist in multiple‐good models. We estimate them jointly with a brand‐level demand system to evaluate the total impact of a brand manager's price change on own quantity. In a differentiated product market, this is a useful addition to a partial demand elasticity approach, because a change in one brand's price typically engenders a price reaction by other brands that affects own quantity via substantial cross‐price elasticities among substitutes. Strategic pricing in the Boston fluid milk market was also influenced by the existence of a raw milk price support program, the Northeast Dairy Compact. We find that the advent of the Compact was a focal point event that crystallized a shift away from Nash–Bertrand to more cooperative pricing. If the downstream market is not competitive, one needs to consider strategic price reactions when designing and evaluating agricultural price programs.
Evaluation of an in situ formed synthetic hydrogel as a biodegradable membrane for guided bone regeneration
Authors: Jung Ronald E. , Zwahlen Roger , Weber Franz E. , Molenberg Aart , Van Lenthe G. Harry , Hammerle Christoph H. F.
Published: June 2006

Abstract: The aim of the present study was to test whether or not the application of an in situ formed synthetic hydrogel made of polyethylene glycol (PEG) used as a biodegradable membrane for guided bone regeneration will result in the same amount of bone regeneration as with the use of an expanded polytetrafluoro‐ethylene (ePTFE) membrane. In eight New Zealand White rabbits, four evenly distributed 6 mm diameter defects were drilled into the calvarial bone. Three treatment modalities were evenly distributed among the 32 defects: hydroxyapatite (HA)/tricalciumphosphate (TCP) granules covered at the outer and inner surface with a PEG membrane (test), HA/TCP granules covered at the outer and inner surface with an ePTFE membrane (positive control) and HA/TCP granules alone without membranes (negative control). After 4 weeks, the animals were sacrificed and the calvarial bones were removed. The area fraction of newly formed bone was determined by histomorphometrical analysis of the vertical sections from the middle of the defect and by micro‐computed tomography of the entire defect. Multiple regression analysis (SAS® GLM) was used to model the amount of new bone formation. The quantitative histomorphometric analysis clearly revealed higher values of newly formed bone for the two membrane groups compared with the negative control group. The average area fractions of newly formed bone measured within the former defect amounted to 20.3±9.5% for the PEG membrane, 18.9±9.9% for the ePTFE membrane, and 7.3±5.3% for the sites with no membrane. The micro‐computed tomography also showed higher values of new bone formation for the PEG and for the ePTFE groups compared with the negative control group. The GLM revealed a highly significant effect of the treatment on the amount of bone formation (P=0.0048). The values for the negative control group were significantly lower than the ones found in the PEG membrane group (P=0.0017), whereas the ePTFE membrane group showed no significant difference from the PEG membrane group. It is concluded that the PEG membrane can be used successfully as a biodegradable barrier membrane in the treatment of non‐critical‐size defects in the rabbit skull, and leads to similar amounts of bone regeneration as an ePTFE membrane.
Horizontal ridge augmentation using autogenous block grafts and the guided bone regeneration technique with collagen membranes: a clinical study with 42 patients
Authors: Von Arx Thomas , Buser Daniel
Published: June 2006

Objective: To analyze the clinical outcome of horizontal ridge augmentation using autogenous block grafts covered with anorganic bovine bone mineral (ABBM) and a bioabsorbable collagen membrane.

Material and methods: In 42 patients with severe horizontal bone atrophy, a staged approach was chosen for implant placement following horizontal ridge augmentation. A block graft was harvested from the symphysis or retromolar area, and secured to the recipient site with fixation screws. The width of the ridge was measured before and after horizontal ridge augmentation. The block graft was subsequently covered with ABBM and a collagen membrane. Following a tension‐free primary wound closure and a mean healing period of 5.8 months, the sites were re‐entered, and the crest width was re‐assessed prior to implant placement.

Results: Fifty‐eight sites were augmented, including 41 sites located in the anterior maxilla. The mean initial crest width measured 3.06 mm. At re‐entry, the mean width of the ridge was 7.66 mm, with a calculated mean gain of horizontal bone thickness of 4.6 mm (range 2–7 mm). Only minor surface resorption of 0.36 mm was observed from augmentation to re‐entry.

Conclusions: The presented technique of ridge augmentation using autogenous block grafts with ABBM filler and collagen membrane coverage demonstrated successful horizontal ridge augmentation with high predictability. The surgical method has been further simplified by using a resorbable membrane. The hydrophilic membrane was easy to apply, and did not cause wound infection in the rare instance of membrane exposure.
Antimicrobial therapy using a local drug delivery system (Arestin®) in the treatment of peri‐implantitis. I: microbiological outcomes
Authors: Persson G. Rutger , Salvi Giovanni E. , Heitz‐Mayfield Lisa J. A. , Lang Niklaus P.
Published: June 2006

Objectives: To assess the microbiological outcome of local administration of minocycline hydrochloride microspheres 1 mg (Arestin®) in cases with peri‐implantitis and with a follow‐up period of 12 months.

Material and methods: After debridement, and local administration of chlorhexidine gel, peri‐implantitis cases were treated with local administration of minocycline microspheres (Arestin®). The DNA–DNA checkerboard hybridization method was used to detect bacterial presence during the first 360 days of therapy.

Results: At Day 10, lower bacterial loads for 6/40 individual bacteria including Actinomyces gerensceriae (P<0.1), Actinomyces israelii (P<0.01), Actinomyces naeslundi type 1 (P<0.01) and type 2 (P<0.03), Actinomyces odontolyticus (P<0.01), Porphyromonas gingivalis (P<0.01) and Treponema socranskii (P<0.01) were found. At Day 360 only the levels of Actinobacillus actinomycetemcomitans were lower than at baseline (mean difference: 1 × 105; SE difference: 0.34 × 105, 95% CI: 0.2 × 105 to 1.2 × 105; P<0.03). Six implants were lost between Days 90 and 270. The microbiota was successfully controlled in 48%, and with definitive failures (implant loss and major increase in bacterial levels) in 32% of subjects.

Conclusions: At study endpoint, the impact of Arestin® on A. actinomycetemcomitans was greater than the impact on other pathogens. Up to Day 180 reductions in levels of Tannerella forsythia, P. gingivalis, and Treponema denticola were also found. Failures in treatment could not be associated with the presence of specific pathogens or by the total bacterial load at baseline. Statistical power analysis suggested that a case control study would require approximately 200 subjects.
Effects of indomethacin and dexamethasone on mechanical scratching‐induced cutaneous barrier disruption in mice
Authors: Honma Yusuke , Arai Iwao , Sakurai Takanobu , Futaki Nobuko , Hashimoto Yuki , Sugimoto Masanori , Nakanishi Yutaka , Nakaike Shiro
Published: June 2006

Abstract:  Effects of indomethacin and dexamethasone on recovery of cutaneous barrier disruption induced by mechanical scratching were examined. Cutaneous barrier was disrupted by scratching using a stainless‐steel wire brush (mechanical scratching) and compared to cutaneous application of acetone/ether (1 : 1) mixture (AE) and tape‐stripping. Increase of transepidermal water loss (TEWL), as an indicator of a broken skin barrier, and recovery period for mechanical scratching were higher and longer than those for AE treatment and tape‐stripping and we also confirmed the severity of skin damage in a histological study. Topical application of moisturizers showed a temporal effect, rapidly decreased TEWL on mechanical scratching‐ or AE treatment‐induced cutaneous barrier disruption, and gradually increased base levels from 4 to 12 h after treatment. Topical application of indomethacin or dexamethasone prolonged the recovery period for the cutaneous barrier, and concomitant use further worsened the status of the barrier. Additionally, we examined the effects of prostaglandins (PGs) and inflammatory cytokine on mechanical scratching‐induced cutaneous barrier disruption pretreated with indomethacin and dexamethasone. As a results, PGD2 and interleukin (IL)‐1β significantly accelerated the recovery of cutaneous barrier disruption by mechanical scratching but such was not the case with PGE2, IL‐1α, and tumor necrosis factor‐α treatment. These results suggest that indomethacin and dexamethasone prolonged the recovery period caused by inhibition of PGD2 and IL‐1β. Mechanical scratching‐induced cutaneous barrier disruption may be a useful method for evaluating means of recovery from skin damage.
Baseline and stimulated turnover of cell surface c‐Kit expression in different types of human mast cells
Authors: Babina Magda , Rex Claudia , Guhl Sven , Thienemann Friedrich , Artuc Metin , Henz Beate M. , Zuberbier Torsten
Published: June 2006

Abstract:  The receptor tyrosine kinase c‐Kit is fundamental to mast cell (MC) development and maintenance. Its regulation can occur at various levels, but nothing is known about how this is accomplished in normal human tissue MC. Likewise, the baseline turnover of c‐Kit has not been addressed yet. We used mature MC from human skin, along with the MC lines LAD‐2 and HMC‐1 and treated them with stem cell factor (SCF), cycloheximide, actinomycin D (AD) and combinations thereof, and determined expression levels of c‐Kit and other surface receptors by flow cytometry. Ligand‐induced internalization of c‐Kit was found to be a universal mechanism and detectable in all MC subtypes. By Western blot analysis of LAD‐2 cells, c‐Kit was found to nearly disappear 3 h after the addition of SCF to slowly recover thereafter. Investigations into the baseline turnover of c‐Kit expression revealed that c‐Kit is strongly affected by the inhibition of de novo translation in all MC subsets, while a suppression of transcription had a weaker effect and displayed greater cell‐to‐cell variation. Only a minor impact on other cell surface receptors (CD29, CD50 and CD54) was noted. On combined treatment, cycloheximide, AD and SCF displayed additive effects, resulting in a complete disappearance of c‐Kit from the cell surface. In conclusion, c‐Kit represents a rapidly cycling cell surface receptor. It is not only immediately internalized upon binding of its ligand, but it is also heavily affected by the inhibition of translation or transcription when viewed against an average background. Interestingly, c‐Kit regulation seems largely independent of the MC subtype.
A short English version of the Fear of Dental Pain questionnaire
Authors: Van Wijk Arjen J. , McNeil Daniel W. , Ho Cornelia J. , Buchanan Heather , Hoogstraten Johan
Published: June 2006

Fear of dental pain is a highly relevant covariate in dental pain research. The present study was designed to develop a short version of the Fear of Dental Pain questionnaire (FDPQ) in order to facilitate research in this area. The original 18‐item FDPQ was translated from Dutch to English, and data from previously published and unpublished studies (all Dutch‐speaking subjects) were used to examine psychometric properties (n = 960). A short version was constructed based on psychometric properties and face validity of the items. Five items were selected for a short FDPQ. A strong correlation was found between the original and the short version (r = 0.96). Factor analysis revealed a one‐dimensional solution, explaining ≈ 76% of the variance, with high internal consistency (alpha = 0.87). The short FDPQ allows rapid identification, by dentists, of patients who may require special attention, longer appointments, and specific dental pain management. In addition, it would assist in the development and evaluation of tailored interventions aimed at this group.
Influence of whitening on the degree of conversion of dental adhesives on dentin
Authors: Cadenaro Milena , Breschi Lorenzo , Antoniolli Francesca , Mazzoni Annalisa , Di Lenarda Roberto
Published: June 2006

The aim of this study was to analyze the extent of polymerization of different adhesive systems on whitened dentin. One adhesive of each class was investigated: Adper Scotchbond Multi Purpose (3M ESPE); One‐Step (Bisco); Clearfil Protect Bond (Kuraray); and Xeno III (Dentsply DeTrey). Dentin disks were treated with Opalescence Xtra Boost (Ultradent) for 30 min and bonded immediately after 24 h or after 14 d of storage in 100% humidity at 37°C. Unbleached dentin disks were prepared as controls. The extent of polymerization of bonded interfaces was obtained with differential scanning calorimetry (DSC) at 20, 40 and 60 s, and the data were statistically analyzed. The extent of polymerization obtained from DSC exotherms of adhesives applied immediately after whitening was significantly lower compared with controls. An increased extent of polymerization after storage was confirmed for all adhesives, and no difference with controls was found after 14 d. A prolonged irradiation time increased the curing rate for all the tested adhesives. This study supports the hypothesis that polymerization of the adhesive is reduced after dentin whitening and that delayed adhesive application reverses the polymerization inhibition. Prolonged polymerization intervals may counteract the inhibition of polymerization caused by the whitening procedure. Nevertheless, further in vivo studies should validate this issue.
Effect of stannous fluoride toothpaste on erosion‐like lesions: an in vivo study
Authors: Young Alix , Thrane Per S. , Saxegaard Erik , Jonski Grazyna , Rölla Gunnar
Published: June 2006

It has recently been shown that stannous fluoride (SnF2), in the form of aqueous solutions and as toothpaste, can reduce the dissolution of enamel in erosive acids in vitro and in situ. The aim of this study was to compare the effect of toothpastes containing SnF2 or NaF on enamel dissolution using an in vivo model. Four healthy anterior teeth in each subject (n = 20) were exposed to diluted citric acid (100 mmol l−1 or 10 mmol l−1) applied using a peristaltic pump (5 ml @7 ml min−1) and the acid was collected in a test tube before and after application of the respective toothpastes (etch I and etch II). Toothpaste was applied to the labial surfaces with a soft brush (four applications, each of 1‐min duration), with gentle water rinsing between applications. Each subject had one pair of teeth treated with each of the test toothpastes. Enamel dissolution was examined by assessment of calcium content in the citric acid applied before and after the treatment with toothpaste. The results indicate that the SnF2 toothpaste markedly reduced the dissolution of teeth in vivo (etch II < etch I), whereas the NaF toothpaste provided no protection (etch II > etch I). Toothpaste appears to be an acceptable vehicle for SnF2 and maintains the dissolution‐reducing effect exhibited by aqueous solutions of this fluoride salt.
Effect of controlled early implant loading on bone healing and bone mass in guinea pigs, as assessed by micro‐CT and histology
Authors: De Smet Els , Jaecques Siegfried V. N. , Wevers Martine , Jansen John A. , Jacobs Reinhilde , Sloten Jos Vander , Naert Ignace E.
Published: June 2006

Without controlled loading, the failure of early loaded oral implants is higher than in delayed loading, unless loading regimens can be identified that stimulate bone formation. The purpose of this study was to investigate whether controlled early loading optimizes osseointegration. Six series of guinea pigs received percutaneous implants in both tibiae. One implant was stimulated, the contra‐lateral served as the control. The strain rate amplitude varied from 1,620 to 12,000 µstrain s−1. In vivo microfocus computed tomography (micro‐CT) was used to study the peri‐implant bone at three time points: 1 wk after implantation, but before starting stimulation (V1); 2 wk after stimulation (V2); and 4 wk after stimulation, after the guinea pigs were killed (PM). Bone implant contact and bone mass [BM (%) bone occupied area fraction] were analyzed. The implant failure was 5.9% (six control/one test). Although bone implant contact did not significantly differ, bone mass in the distal half peri‐implant marrow cavity was significantly higher around test implants. Strain rate amplitude and the difference in bone mass between test and control implants were inversely correlated. A strain rate amplitude of 1,620 µstrain s−1 in the cortical bone at a distance of 1.3 mm from the implant showed the highest effect. Based on these results, early loading did not negatively affect the implant outcome. On the contrary, an improved bone reaction in the marrow cavity around early loaded implants was achieved.
In vitro biofilm formation on the surface of resin‐based dentine adhesives
Authors: Rolland Sarah L. , McCabe John F. , Robinson Colin , Walls Angus W. G.
Published: June 2006

Prevention of root caries on exposed root surfaces in the aging population is a significant challenge. Bonding resins can be applied to exposed root surfaces as sealants; however, minimal data exists regarding biofilm formation on the surface of these resins. We hypothesized that an antibacterial dentine‐bonding resin containing methacryloxydodecyl‐pyridiniumbromide (MDPB) may reduce biofilm formation. Biofilms were produced in pooled stimulated natural whole saliva, supplemented with 1% sucrose, on the surface of 5 dentine‐bonding resins (Clearfil SE, OptiBond Solo, Protect Bond, Protect Bond Primer, and Xeno III) using untreated root surfaces as controls. Biofilms were stained using the Live:Dead Baclight bacterial viability stain, viewed with confocal microscopy, and analyzed using ImageJ image‐analysis software. Resin surfaces encouraged attachment of live bacteria compared with root surfaces. All resins showed similar bacterial colonization in sections adjacent to the resin surface, but in the central and outer portions of biofilms, Xeno III and Protect Bond Primer showed a viable bacterial load similar to that of the root surface. Fluoride‐releasing resins (OptiBond Solo/Protect Bond) did not show reduced biofilm formation. Thus, antibacterial agents within the resins have a minimal effect on biofilm formation, particularly when directly adjacent to the root surface.
The Crystal Structure of the C‐Terminal Domain of Vps28 Reveals a Conserved Surface Required for Vps20 Recruitment
Authors: Pineda‐Molina Estela , Belrhali Hassan , Piefer Andrew J. , Akula Indira , Bates Paul , Weissenhorn Winfried
Published: June 2006

The endosomal sorting complex I required for transport (ESCRT‐I) is composed of the three subunits Vps23/Tsg101, Vps28 and Vps37. ESCRT‐I is recruited to cellular membranes during multivesicular endosome biogenesis and by enveloped viruses such as HIV‐1 to mediate budding from the cell. Here, we describe the crystal structure of a conserved C‐terminal domain from Sacharomyces cerevisiae Vps28 (Vps28‐CTD) at 3.05 Å resolution which folds independently into a four‐helical bundle structure. Co‐expression experiments of Vps28‐CTD, Vps23 and Vps37 suggest that Vps28‐CTD does not directly participate in ESCRT‐I assembly and may thus act as an adaptor module for downstream interaction partners. We show through mutagenesis studies that Vps28‐CTD employs its strictly conserved surface in the interaction with the ESCRT‐III factor Vps20. Furthermore, we present evidence that Vps28‐CTD is sufficient to rescue an equine infectious anaemia virus (EIAV) Gag late domain deletion. Vps28‐CTD mutations abolishing Vps20 interaction in vitro also prevent the rescue of the EIAV Gag late domain mutant consistent with a potential direct Vps28‐ESCRT‐III Vps20 recruitment. Therefore, the physiological relevant EIAV Gag–Alix interaction can be functionally replaced by a Gag‐Vps28‐CTD fusion. Because both Alix and Vps28‐CTD can directly recruit ESCRT‐III proteins, ESCRT‐III assembly coupled to Vps4 action may therefore constitute the minimal budding machinery for EIAV release.
Between Hoax and Hope: Miscegenation and Nineteenth‐Century Interracial Romance
Authors: Ings Katharine Nicholson
Published: June 2006

This essay surveys recent scholarship on interracial romance during the nineteenth century using the hoax Miscegenation pamphlet of 1863 as a lens. An anonymous and ironic piece of writing that promoted race‐mixing from a deceptively Republican perspective, Miscegenation coined the titular term, newly situating interracial relationships within a Latinate, pseudo‐scientific framework. It also encouraged romance between white women and black men, an endorsement that was designed to enrage its white male readership but in fact gave hope to some white women who were unable to articulate their interracial desire publicly. Using this double focus, I explore how nineteenth‐century authors of interracial romance borrowed the language of science, such as “hybridity” and “crossing”; how they employed the concept of “blood‐mixing” as both sexual and medicinal (via transfusions); and I read the Miscegenation pamphlet as a kind of scientific romance fiction itself.
Persistent patterns in accretion discs
Authors: Amin Mustafa A. , Frolov Andrei V.
Published: June 2006

We present a set of new characteristic frequencies associated with accretion discs around compact objects. These frequencies arise from persistent rotating patterns in the disc that are finite in radial extent and driven purely by the gravity of the central body. Their existence depends on general relativistic corrections to orbital motion and, if observed, could be used to probe the strong gravity region around a black hole. We also discuss a possible connection to the puzzle of quasi-periodic oscillations.
The late time evolution of gamma-ray bursts: ending hyperaccretion and producing flares
Authors: Proga Daniel , Zhang Bing
Published: June 2006

We consider the properties of a hyperaccretion model for gamma-ray bursts (GRBs) at late times when the mass supply rate is expected to decrease with time. We point out that the region in the vicinity of the accretor and the accretor itself can play an important role in determining the rate of accretion, and its time behaviour, and ultimately the energy output. Motivated by numerical simulations and theoretical results, we conjecture that the energy release can be repeatedly stopped and then restarted by the magnetic flux accumulated around the accretor. We propose that the episode or episodes when the accretion resumes correspond to X-ray flares discovered recently in a number of GRBs.
Nutrient enrichment weakens the stabilizing effect of species richness
Authors: Romanuk Tamara N. , Vogt Richard J. , Kolasa Jurek
Published: June 2006

With global freshwater biodiversity declining at an even faster rate than in the most disturbed terrestrial ecosystems, understanding the effects of changing environmental conditions on relationships between biodiversity and the variability of community and population processes in aquatic ecosystems is of significant interest. Evidence is accumulating that biodiversity loss results in more variable communities; however, the mechanisms underlying this effect have been the subject of considerable debate. We manipulated species richness and nutrients in outdoor aquatic microcosms composed of naturally occurring assemblages of zooplankton and benthic invertebrates to determine how the relationship between species richness and variability might change under different nutrient conditions. Temporal variability of populations and communities decreased with increasing species richness in low nutrient microcosms. In contrast, we found no relationship between species richness and either population or community variability in nutrient enriched microcosms. Of the different mechanisms we investigated (e.g. overyielding, statistical averaging, insurance effects, and the stabilizing effect of species richness on populations) the only one that was consistent with our results was that increases in species richness led to more stable community abundances through the stabilizing effect of species richness on the component populations. While we cannot conclusively determine the mechanism(s) by which species richness stabilized populations, our results suggest that more complete resource‐use in the more species‐rich low nutrient communities may have dampened population fluctuations.
Hydrodynamic Performance of a Novel Design of Pressurized Fluidized Bed Combustor
Authors: Wang Alan L. T. , Stubington John F. , Xu Jiangang
Published: June 2006

A bench-scale fluidized bed combustor with a novel fluidizing gas injection manifold was successfully built for characterization of Australian black coals under PFBC conditions. Instead of the usual horizontal distributor plate to support the bed and distribute the fluidizing gas, the fluidizing gas was injected horizontally through 8 radial ports in the cylindrical wall of the combustor. To verify satisfactory hydrodynamic performance with the novel gas injection manifold, the fluidization was directly investigated by measuring differential pressure fluctuations under both ambient and PFBC conditions. In addition, a Perspex cold model was built to simulate the hydrodynamics of the hot bed in the PFBC facility. Under PFBC conditions, the bed operated in a stable bubbling regime and the solids were well mixed. The bubbles in the bed were effectively cloudless and no gas backmixing or slugging occurred; so the gas flow in the bed could be modeled by assuming two phases with plug flow through each phase. The ratio of Umf for the simulated bed to Umf for the hot PFBC bed matched the conditions proposed by Glicksman’s scaling laws. The bubbles rose along the bed with axial and lateral movements, and erupted from the bed surface evenly and randomly at different locations. Two patterns of particle movement were observed in the cold model bed: a circular pattern near the top section and a rising and falling pattern dominating in the lower section.
The Study of Partitioning of Heavy Metals During Fluidized Bed Combustion of Sewage Sludge and Coal
Authors: Gulyurtlu I. , Lopes M. Helena , Abelha P. , Cabrita I. , Oliveira J. F. Santos
Published: June 2006

The behavior of Cd, Cr, Cu, Co, Mn, Ni, Pb, Zn, and Hg during the combustion tests of a dry granular sewage sludge on a fluidized bed combustor pilot (FBC) of about 0.3 MW was evaluated. The emissions of these heavy metals from mono-combustion were compared with those of co-combustion of the sludge with a bituminous coal. The effect of the addition of limestone was also studied in order to retain sulphur compounds and to verify its influence on the retention of heavy metals (HM). Heavy metals were collected and analyzed from different locations of the installation, which included the stack, the two cyclones, and the material removed from the bed. The results showed that the volatility of metals was rather low, resulting in emissions below the legal limits of the new directive on incineration, with the exception of Hg during the mono-combustion tests. The partitioning of metals, except for Hg, appeared to follow that of ashes, amounting to levels above 90% in the bed streams in the mono-combustion case. For co-combustion, there was a lower fixation of HM in the bed ashes, mostly originating essentially from the sewage sludge, ranging between 40% and 80%. It is believed that in this latter case, a slightly higher temperature could have enhanced the volatilization, especially of Cd and Pb. However these metals were then retained in fly ashes captured in the cyclones. In the case of Hg, the volatilisation was complete. The bed ashes were free of Hg and part of Hg was retained in the cyclones and the rest was emitted either with fine ash particles or in gaseous forms. In mono-combustion the Hg emissions from the stack (particles and gas) accounted for about 50%, although there was a significant amount unaccounted for. This appeared to have significantly decreased in the case of co-combustion, as only about 15% has been emitted, due to the retention effect of cyclone ashes which presented high quantities of unburned matter, calcium and sulphur.
Ash Cooling Screws—A Retrospective and Looking Ahead
Authors: Kerner Jeff W. , Stetler Gary W.
Published: June 2006

The first commercial screw cooler on record for cooling bottom ash from fluidized bed combustion (FBC) boilers was installed in 1979. Since then, over 300 ash screw cooler (ASC) machines have been used for this duty worldwide. The relatively quick upsurge in developing and building FBC boilers in the early 1980s forced the industry to select existing cooling screw designs, typically used in less severe services in the chemical, grain, plastics, and food industry. At the time, these were the only reasonable and readily available machines thought capable of handling abrasive, corrosive, and extremely hot bottom ash. The extreme difficulties of operating and maintaining these units in this service quickly became apparent, but only after quite a number of initial designs had already been designed, purchased, and installed. Today, 23 years later, both the manufacturers and users of ASCs can look back and point to installations where, thanks to communication and cooperation between operators and the manufacturer, operating units and their installations have been successfully modified, resulting in smoother operation and much less frequent maintenance. New units can incorporate a range of features, depending upon the anticipated ash quality. As a result, ASCs are now reportedly ranked low on the list of FBC operators and managers concerns. This paper will address what has been learned by both manufacturers and operators. The results of a survey of the operating and maintenance experience as well as maintenance costs of a wide sample of ASC users will be presented. A look ahead as to where ash screw cooler technology is moving is addressed, with help and continued input from current users of the equipment.
The Implications of Burning a Blend of Waste Materials in a Fluidizied Bed Combustor
Authors: Gulyurtlu I. , Abelha P. , Boavida D. , Seabra J. , Gomes S. , Chaleta N. , Cabrita I.
Published: June 2006

A mixture involving wood, plastics, paper, and textile materials was burned in a fluidized bed combustor to monitor the gaseous emissions and to analyze the ashes collected in different locations of the installation. The ashes collected were first analyzed to verify the partitioning of heavy metals in different ash streams. They were then subjected to leaching tests to verify the solubility of different components present. There is a growing interest in utilizing wastes, which cannot be recycled for further use, for energy, particularly in Europe as the amounts are great and the cost of depositing them in landfills has become very considerable. These wastes are considered renewable sources and the recent policy is to encourage their use for energy, especially for decentralized energy production. However, these wastes may be contaminated and have to be verified that their utilization for energy does not bring about any adverse consequences on the environment. Each component making up the blend to be used as fuel needs to be analyzed to determine not only its composition but also its heating value so that the final blend to be prepared could present minimum risk for emissions of pollutants, ideally less than coal and with a heating value comparable, at least, to that of coal. The results obtained suggest that (i) the combustion efficiency was very high, (ii) there was an enrichment of ashes with heavy metals in the cyclones compared to the bed material, (iii) the gaseous pollutants were below the permitted limits, and (iv) the ashes did not have tendency for leaching. Such mixtures could, therefore, be used as a solid fuel in industry as a substitution for coal or heavy fuel oil.
Atmospheric Fluidized Bed Combustion (AFBC) Plants: An Operations and Maintenance Study
Authors: Fuller Jack A. , Beavers Harvie , Bessette Robert
Published: June 2006

The authors analyzed data from a fluidized bed boiler survey distributed during the spring of 2003 to develop appropriate AFBC (Atmospheric Fluidized Bed Combustion) performance benchmarks. The survey was sent to members of CIBO (Council of Industrial Boiler Owners), who sponsored the survey, as well as to other firms who had an operating AFBC boiler on-site. There were three primary purposes for the collection and analysis of the data contained in this fluidized bed boiler survey: (1) To develop AFBC benchmarks on technical, cost, revenue, and environmental issues; (2) to inform AFBC owners and operators of contemporary concerns and issues in the industry; (3) to improve decision making in the industry with respect to current and future plant start-ups and ongoing operations.
The Study of Combustion of Municipal Waste in a Fluidized Bed Combustor
Authors: Gulyurtlu I. , Crujeira T. , Lopes M. H. , Abelha P. , Boavida D. , Seabra J. , Gonçalves R. , Sargaço C. , Cabrita I.
Published: June 2006

The combustion behavior of municipal solid waste was studied in a pilot fluidized bed combustor. The waste was pelletized prior to its use. Both co-firing with coal and combustion of waste alone were under taken. The combustion studies were carried out on the pilot installation of INETI. The fluidized bed combustor is square in cross section with each side being 300mm long. Its height is 5000mm. There is a second air supply to the freeboard at different heights to deal with high volatile fuels. There was a continuous monitoring of the temperatures in the bed, as well as the composition of the combustion gases. The combustion gases leaving the reactor were let go through the recycling cyclone first to capture most of particulates elutriated out of the combustor. There was a second cyclone, which was employed with the aim of increasing the overall efficiency of collecting solid particles. The gaseous pollutants leaving the stack were sampled under isokinetic conditions for particulate matter, chlorine compounds, and heavy metals. The ash streams were characterized for heavy metals. The results obtained were compared with national legislation. The results obtained suggest that (i) the combustion efficiency was very high, (ii) there was an enrichment of ashes with heavy metals in the cyclones compared to the bed material, (iii) in general, the flue gas emissions were below the permited limits, and (iv) for the compliance with the new European directive for stricter emission limits adequate control devices, like bag filters, should be integrated with refuse derived fuel (RDF) combustion.
Functional Characterization of
Aspergillus nidulans
Homologues of
Saccharomyces cerevisiae
Spa2 and Bud6
Authors: Virag Aleksandra , Harris Steven D.
Published: June 2006

The importance of polarized growth for fungi has elicited significant effort directed at better understanding underlying mechanisms of polarization, with a focus on yeast systems. At sites of tip growth, multiple protein complexes assemble and coordinate to ensure that incoming building material reaches the appropriate destination sites, and polarized growth is maintained. One of these complexes is the polarisome that consists of Spa2, Bud6, Pea2, and Bni1 in
Saccharomyces cerevisiae
. Filamentous hyphae differ in their development and life style from yeasts and likely regulate polarized growth in a different way. This is expected to reflect on the composition and presence of protein complexes that assemble at the hyphal tip. In this study we searched for polarisome homologues in the model filamentous fungus
Aspergillus nidulans
and characterized the
S. cerevisiae
Spa2 and Bud6 homologues, SpaA and BudA. Compared to the
S. cerevisiae
Spa2, SpaA lacks domain II but has three additional domains that are conserved within filamentous fungi. Gene replacement strains and localization studies show that SpaA functions exclusively at the hyphal tip, while BudA functions at sites of septum formation and possibly at hyphal tips. We show that SpaA is not required for the assembly or maintenance of the Spitzenkörper. We propose that the core function of the polarisome in polarized growth is maintained but with different contributions of polarisome components to the process.