bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulation of Taylor-Couette flow. Part 2. Numerical results for wavy-vortex flow with one travelling wave
Authors: Marcus Philip S.
Published: April 2006

We use a numerical method that was described in Part 1 (Marcus 1984a) to solve the time-dependent Navier-Stokes equation and boundary conditions that govern Taylor-Couette flow. We compute several stable axisymmetric Taylor-vortex equilibria and several stable non-axisymmetric wavy-vortex flows that correspond to one travelling wave. For each flow we compute the energy, angular momentum, torque, wave speed, energy dissipation rate, enstrophy, and energy and enstrophy spectra. We also plot several 2-dimensional projections of the velocity field. Using the results of the numerical calculations, we conjecture that the travelling waves are a secondary instability caused by the strong radial motion in the outflow boundaries of the Taylor vortices and are not shear instabilities associated with inflection points of the azimuthal flow. We demonstrate numerically that, at the critical Reynolds number where Taylor-vortex flow becomes unstable to wavy-vortex flow, the speed of the travelling wave is equal to the azimuthal angular velocity of the fluid at the centre of the Taylor vortices. For Reynolds numbers larger than the critical value, the travelling waves have their maximum amplitude at the comoving surface, where the comoving surface is defined to be the surface of fluid that has the same azimuthal velocity as the velocity of the travelling wave. We propose a model that explains the numerically discovered fact that both Taylor-vortex flow and the one-travelling-wave flow have exponential energy spectra such that In [E(k)] ∝ k1, where k is the Fourier harmonic number in the axial direction.
Numerical solution of free-boundary problems in fluid mechanics. Part 3. Bubble deformation in an axisymmetric straining flow
Authors: Ryskin G. , Leal L. G.
Published: April 2006

We consider the deformation of a bubble in a uniaxial extensional flow for Reynolds numbers in the range 0.1 [les ] R [les ] 100. The computations show that the bubble bursts at a relatively early stage of deformation for R [ges ] O(10), never reaching the highly elongated shapes observed and predicted at lower Reynolds numbers. We also compute the deformation of the bubble under the assumption of potential flow, and conclude that the potential-flow solution provides a good approximation to the real flow in this case for R [ges ] O(100).
Contaminant dispersion as viewed from a fixed position
Authors: Smith Ronald
Published: April 2006

A Hermite series expansion is used to describe the time evolution of the contaminant concentration at a fixed location in a flow. Exact expressions are derived for the dosage, centroid and temporal variance. A two-mode approximation is proposed which gives accurate results at moderate to large distances downstream of the discharge.
Dispersion in fixed beds
Authors: Koch Donald L. , Brady John F.
Published: April 2006

A macroscopic equation of mass conservation is obtained by ensemble-averaging the basic conservation laws in a porous medium. In the long-time limit this ‘macro-transport’ equation takes the form of a macroscopic Fick's law with a constant effective diffusivity tensor. An asymptotic analysis in low volume fraction of the effective diffusivity in a bed of fixed spheres is carried out for all values of the Péclet number ℙ = Ua/Df, where U is the average velocity through the bed. a is the particle radius and Df is the molecular diffusivity of the solute in the fluid. Several physical mechanisms causing dispersion are revealed by this analysis. The stochastic velocity fluctuations induced in the fluid by the randomly positioned bed particles give rise to a convectively driven contribution to dispersion. At high Péclet numbers, this convective dispersion mechanism is purely mechanical, and the resulting effective diffusivities are independent of molecular diffusion and grow linearly with ℙ. The region of zero velocity in and near the bed particles gives rise to non-mechanical dispersion mechanisms that dominate the longitudinal diffusivity at very high Péclet numbers. One such mechanism involves the retention of the diffusing species in permeable particles, from which it can escape only by molecular diffusion, leading to a diffusion coefficient that grows as ℙ2. Even if the bed particles are impermeable, non-mechanical contributions that grow as ℙ ln ℙ and ℙ2 at high ℙ arise from a diffusive boundary layer near the solid surfaces and from regions of closed streamlines respectively. The results for the longitudinal and transverse effective diffusivities as functions of the Péclet number are summarized in tabular form in §6. Because the same physical mechanisms promote dispersion in dilute and dense fixed beds, the predicted Péclet-number dependences of the effective diffusivities are applicable to all porous media. The theoretical predictions are compared with experiments in densely packed beds of impermeable particles, and the agreement is shown to be remarkably good.
The deflection of a baroclinic jet by a wall in a rotating fluid
Authors: Whitehead J. A.
Published: April 2006

The momentum integral of a baroclinic jet of fluid in a rotating frame determines the relative size of two jets which are produced when the jet is split by a wall. Owing to lateral variation of velocity and depth of the jet, the percentage of fluid which goes to the right or left differs from that of the non-rotating jet, which is generally assumed to have no shear. For a northern hemisphere jet of zero or constant potential vorticity, much more fluid flows to the right than to the left; for a jet normal to the wall more than 65% goes to the right and less than 35% to the left.
Role of membrane viscosity in the orientation and deformation of a spherical capsule suspended in shear flow
Authors: Barthes-Biesel D. , Sgaier H.
Published: April 2006

Red blood cells or artificial vesicles may be conveniently represented by capsules, i.e. liquid droplets surrounded by deformable membranes. The aim of this paper is to assess the importance of viscoelastic properties of the membrane on the motion of a capsule freely suspended in a viscous liquid subjected to shear flow. A regular perturbation solution of the general problem is obtained when the particle is initially spherical and undergoing small deformations. With a purely viscous membrane (infinite relaxation time) the capsule deforms into an ellipsoid and has a continuous flipping motion. When the membrane relaxation time is of the same order as the shear time, the particle reaches a steady ellipsoidal shape which is oriented with respect to streamlines at an angle that varies between 45° and 0°, and decreases with increasing shear rates. Furthermore it is predicted that the deformation reaches a maximum value, which is consistent with experimental observations of red blood cells.
Characteristics of the flow around conventional and supercritical airfoils
Authors: Nakayama A.
Published: April 2006

Measurements of the mean and fluctuating velocities have been obtained with pressure and hot-wire probes in the attached boundary layers and wakes of two airfoil models at a low Mach number. The first model is a conventional airfoil at zero incidence and the second an advanced supercritical airfoil at an angle of attack of 4°. The mean-flow and Reynolds-stress data and related quantities are presented with emphasis on the trailing-edge region. The results indicate that the flow around the conventional airfoil is a minor perturbation of a symmetric flat-plate flow with small wake curvature and weak viscous–inviscid interaction. The flow around the supercritical airfoil is in considerable contrast with strong streamwise pressure gradients, non-negligible normal pressure gradients, and large surface and streamline curvatures of the trailing-edge flow. The near wake is strongly curved and intense mixing occurs between the retarded upper-surface boundary layer and strongly accelerated lower-surface boundary layer.
The effect of large-eddy breakup devices on oncoming vorticity
Authors: Dowling A. P.
Published: April 2006

Experiments have shown that a large-eddy breakup device consisting of a short splitter plate placed in the turbulent boundary layer over a plane wall can lead to a reduction in drag. We investigate the idealized problem of an incident line vortex convected past such a device. The vorticity shed from the trailing edge of the plate is found to cancel the effect of the incident vortex and to reduce velocity fluctuations significantly in the vicinity of the wall.
Barrier layers in the subtropical gyres of the world's oceans
Authors: Sato Kanako , Suga Toshio , Hanawa Kimio
Published: April 2006

Barrier layers (BLs) in the subtropical gyres of the world's oceans are detected using all temperature and salinity profiles obtained by Argo floats from Jan. 2000 to Jun. 2005. The synoptic BLs are distributed patchily in the area where climatological BLs are continuously distributed. They are thicker and occur more frequently during Jan.–Apr. (Jul.–Nov.) in the Northern (Southern) Hemisphere with some differences in thickness and occurrence rates among the oceans. We suggest that the same formation mechanism of BLs as that in the North Pacific, i.e., the subduction of high salinity water at sharp salinity fronts on a small scale of approximately 100 km is at work in the other subtropical gyres. Seasonal change of the mixed layer depth contributes to the seasonality of BL thickness and frequency in all subtropical gyres.
Low-frequency currents induced in adjacent spherical cells
Authors: Margetis Dionisios , Savva Nikos
Published: April 2006

The currents induced inside cells by external electric fields in the frequency range 50–60 Hz are studied analytically by accounting for thin cell membranes with transverse conductivity that is small compared to the conductivity of the saline fluid. A general perturbation scheme is formulated and applied to two adjacent spherical cells of equal radii by using a reflection principle and solving a nonlinear difference equation. The presence of the second cell is found to cause a no more than 10% increase to the current induced in an isolated spherical cell.
Despun rocket borne imager: Design aspects of a space based optical imaging instrument for auroral studies
Authors: Ellis Armin T. , Lessard Marc R. , Bartel Paul , Disbrow Mike , Riley Paul
Published: April 2006

Imaging the aurora from space is scientifically rewarding since understanding the fluctuations in conjunction with other parameters measured along the magnetic field line of interest can resolve ambiguities regarding the nature of the emissions as well as provide a context for the emissions. Typical payloads launched on sounding rockets for auroral studies are spin stabilized, which imply that standard imaging techniques cannot be used due to severe blurring. The despun rocket borne imager is a simple instrumentation concept that uses a Dove prism to counter the rotation effects of the spinning platform and thus produce images without blurring. This technique has been applied to two instruments flown on sounding rockets with varying optical properties needed to address specific scientific queries. This article discusses the design of both of these instruments and includes the necessary considerations for a generic instrument for future projects.
Benefits of treating a sandy soil with a crosslinked-type polyacrylamide
Authors: Sivapalan S.
Published: April 2006

The productivity of sandy soils is mostly limited by their low water-holding capacity and excessive deep percolation losses, which reduce the efficiency of water and fertiliser use by plants. The effect of a crosslinked-type polyacrylamide, ALCOSORB 400, on water-holding capacity of a sandy soil, siliceous sands, was studied under the laboratory and glasshouse conditions. Water-holding capacity of the soil exposed to 0.01 MPa increased by 23 and 95% by adding 0.03 and 0.07% of polyacrylamide to the soil, respectively. This indicated that the soil treated with polyacrylamide was able to store more water than untreated soil, thereby reducing the potential losses due to deep percolation in sandy soils. However, the polyacrylamide in the treated soil did not significantly increase the quantity of water released from the soil by increasing the pressure from 0.01 to 1.5 MPa. The results from the first glasshouse experiment demonstrated that the excess amount of water stored in the soil by polyacrylamide was available to plants and resulted in higher water use and grain production. Consequently, there was a 12 and 18 fold increase in water use efficiency of soybean plants grown in soils treated with 0.03 and 0.07% polyacrylamide, respectively. The results from the second glasshouse experiment demonstrated that increasing amounts of polyacrylamides in a sandy soil can extend the irrigation interval without any adverse effect on the grain yield of soybeans.
Flavobacterium soli sp. nov., isolated from soil
Authors: Yoon Jung-Hoon , Kang So-Jung , Oh Tae-Kwang
Published: April 2006

A Gram-negative, rod-shaped Flavobacterium-like bacterial strain, DS-6T, was isolated from soil from the island of Dokdo, Korea, and subjected to a polyphasic taxonomic study. Strain DS-6T grew optimally at pH 7.0 and 25 °C in the presence of 0–0.5 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 36.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain DS-6T belonged to the genus Flavobacterium. Levels of 16S rRNA gene sequence similarity between strain DS-6T and the type strains of Flavobacterium species were below 95.4 %. Strain DS-6T differed from some phylogenetically related Flavobacterium species in several phenotypic characteristics. On the basis of phenotypic and phylogenetic distinctiveness, DS-6T (=KCTC 12542T=CIP 108840T) was classified in the genus Flavobacterium as the type strain of a novel species, for which the name Flavobacterium soli sp. nov. is proposed.
Estimating the local mean for Bayesian maximum entropy by generalized least squares and maximum likelihood, and an application to the spatial analysis of a censored soil variable
Authors: Orton T. G. , Lark R. M.
Published: April 2006

The Bayesian maximum entropy (BME) method is a valuable tool, with rigorous theoretical underpinnings, with which to predict with soft (imprecise) data. The methodology uses a general knowledge base to derive a joint prior distribution of the data and the prediction by the criterion of maximum entropy; the hard (precise) and soft data are then processed using this prior distribution to yield a posterior distribution that provides the BME prediction. The general knowledge base commonly consists of the mean and covariance functions, which may be extracted from the data. The common method for extracting the mean function from the data is a generalized least squares (GLS) approach. However, when the soft data take the form of intervals of plausible values, this method can result in errors in the BME predictions. This paper suggests a maximum likelihood (ML) method for fitting the local mean. The two methods are compared in terms of their predictions, firstly on simulated random fields and then on a case study to predict the depth of soil using some censored data. The results show that the ML method can result in more accurate BME predictions; the degree of improvement over the GLS method depends on the parameters of the spatial covariance model.
Climate, competition, and the coexistence of island lizards
Authors: BUCKLEY L. B. , ROUGHGARDEN J.
Published: April 2006

The influence of environmental temperatures and competition combine to determine the distributions of island lizards. Neither a bioenergetic model nor simple models of competition alone can account for the distributions. A mechanistic, bioenergetic model successfully predicts how the abundance of a solitaryAnolislizard species will decline along an island's elevation gradient. However, the abundance trends for sympatric lizards diverge from the predictions of the non‐interactive model.

Here we incorporate competition in the bioenergetic model and examine how different forms of competition modify the temperature‐based abundance predictions.

Applying the bioenergetic model with competition to an island chain tests whether the model can successfully predict on which islands two lizards species will coexist.

Coexistence is restricted to the two largest islands, which the model predicts have substantially greater carrying capacities than the smaller islands. The model successfully predicts that competition prevents species coexistence on the smallest islands. However, the model predicts that the mid‐sized islands are capable of supporting substantial populations of both species. Additional island characteristics, such as habitat diversity, resource availability and temporal disturbance patterns, may prevent coexistence.
Immunohistochemical detection of GLUT1, p63 and phosphorylated histone H1 in head and neck squamous intraepithelial neoplasia: evidence for aberrations in hypoxia‐related, cell cycle‐ and stem‐cell‐regulatory pathways
Authors: Burstein D E , Nagi C , Kohtz D S , Lumerman H , Wang B Y
Published: April 2006

Aim : Most epithelial malignancies are characterized by multistep progression from preinvasive/intraepithelial neoplasia to invasive malignancy. Detection and grading of early squamous intraepithelial neoplasia may at times be problematic. The aim of this study was to examine the ability of immunomarkers GLUT1, phospho‐histone H1 and p63 to detect such early lesions.

Methods : Sections of formalin‐fixed paraffin‐embedded tissue from 27 cases of squamous intraepithelial neoplasia, 26 associated with invasive carcinoma, were immunostained with anti‐p63 (4A4; Santa Cruz), anti‐GLUT1 (Chemicon) and anti‐phospho‐histone H1 (monoclonal 12D11) and compared with normal, hyperplastic and immature squamous metaplastic epithelium.

Results : Normal epithelium displayed phospho‐histone H1 in scattered parabasal cells; p63 in the basal one‐quarter to one‐half of epithelium; and GLUT1 negativity or weak/equivocal mid‐epithelial GLUT1+ foci. In hyperplasia phospho‐histone H1+ cells were also limited to the parabasal layer; p63 positivity was essentially identical to that in normal epithelium; GLUT1 characteristically stained basal cells in rete‐like areas. p63 staining in squamous intraepithelial neoplasia (grade 1) was indistinguishable from normal epithelial staining; in contrast, squamous intraepithelial neoplasia (grade 3) was readily apparent, with up to full‐thickness p63 positivity. Squamous intraepithelial neoplasia (grade 1) was readily distinguishable from normal epithelium with both phospho‐histone H1 and GLUT1 immunostaining; both markers were detected in cell layers above the parabasal layer. With both, progressively higher cell layers stained in proportion to the severity of the intraepithelial neoplasia, up to full thickness positivity in grade 3 squamous intraepithelial neoplasia. Squamous metaplasia and grade 3 squamous intraepithelial neoplasia were not distinguishable with p63 (both showed full‐thickness staining) but were readily distinguishable with GLUT1 and phospho‐histone H1 stains. GLUT1 appeared to be the most sensitive marker for all grades of intraepithelial neoplasia.

Conclusion : Altered expression of all three markers was a common finding in squamous intraepithelial neoplasia, hence, dysregulation of cell cycle‐promoting cyclin‐dependent kinases (phospho‐histone H1), altered stem cell regulatory pathways (p63) and enhancement of hypoxia‐sensing pathways (GLUT1) are all early alterations in the progression of squamous malignancy of head and neck origin. A panel of all three may be a useful means of detecting squamous intraepithelial neoplasia.
Anti‐mouse CD154 antibody treatment facilitates generation of mixed xenogeneic rat hematopoietic chimerism, prevents wasting disease and prolongs xenograft survival in mice
Authors: Masaki Hideyuki , Appel Michael C. , Leahy Linda , Leif Jean , Paquin Linda , Shultz Leonard D. , Mordes John P. , Greiner Dale L. , Rossini Aldo A.
Published: April 2006

Masaki H, Appel MC, Leahy L, Leif J, Paquin L, Shultz LD, Mordes JP, Greiner DL, Rossini AA. Anti‐mouse CD154 antibody treatment facilitates generation of mixed xenogeneic rat hematopoietic chimerism, prevents wasting disease and prolongs xenograft survival in mice. Xenotransplantation 2006; 13: 224–232. © Blackwell Munksgaard, 2006

Abstract: Background: The induction of xenogeneic hematopoietic chimerism is an attractive approach for overcoming the host response to xenografts, but establishing xenogeneic chimerism requires severe myeloablative conditioning of the recipient. The goal of this study was to determine if co‐stimulation blockade would facilitate chimerism and xenograft tolerance in irradiation‐conditioned concordant recipients.

Methods: Wistar Furth rat bone marrow (BM) cells were injected into irradiation‐conditioned C57BL/6 mice with or without co‐administration of anti‐mouse CD154 monoclonal antibody (mAb). Chimerism was quantified by flow cytometry, and mice were transplanted with WF rat skin and islet xenografts.

Results: Blockade of CD40–CD154 interaction facilitated establishment of xenogeneic chimerism in mice conditioned with 600 cGy irradiation. Anti‐CD154 mAb was not required for establishment of chimerism in mice treated with 700 cGy. However, mice irradiated with 700 cGy but not treated with anti‐CD154 mAb developed a “graft‐versus‐host disease (GVHD)‐like” wasting syndrome and died, irrespective of their development of chimerism. Xenogeneic chimeras established with irradiation and anti‐CD154 mAb treatment exhibited prolonged skin and, in many cases, permanent islet xenograft survival. Chimerism was unstable and eventually lost in most recipients. Skin xenografts were rejected even in mice that remained chimeric, whereas most islet xenografts survived to the end of the observation period.

Conclusions: Blockade of host CD40–CD154 interaction facilitates the establishment of xenogeneic chimerism and prevents wasting disease and death. Chimerism permits prolonged xenograft survival, but chimerism generated in this way is unstable over time. Skin xenografts are eventually rejected, whereas most islet xenografts survive long term and perhaps permanently.
Monitoring the use of amiodarone: compliance with guidelines
Authors: Burgess C. , Blaikie A. , Ingham T. , Robinson G. , Narasimhan S.
Published: April 2006

Aim: Careful monitoring of amiodarone is recommended because it produces a range of potentially severe adverse effects. The aim of this study was to compare existing practice at our hospitals with the current international guidelines for the use of this drug.

Methods: A retrospective audit was carried out on all patients aged 15 years or older, with a primary discharge diagnosis of tachyarrhythmia and who were commenced and discharged alive on amiodarone between 1 January 2000 and 30 June 2002 from Wellington and Kenepuru Hospitals, Capital and Coast District Health Board, Wellington, New Zealand. The medical records were examined for baseline measurements of renal, liver, thyroid and pulmonary function, the electrocardiogram and chest X‐ray. Follow‐up arrangements were sought postdischarge. A questionnaire was sent to the general practitioner requesting information on follow‐up testing.

Results: During the trial period, 743 patients were admitted with a primary diagnosis of tachyarrhythmia. Eighty‐six patients satisfied the entry criteria, and of these 58 were followed for at least 1 year postdischarge. Baseline testing of the electrocardiogram, full blood count and renal function testing was excellent (95–100%). Chest X‐rays were carried out in 80% of patients. Baseline testing of thyroid (61%) and liver (44%) function was suboptimal. Two percent of patients had pulmonary function testing and no patient had a formal eye examination. At 6 months, only 32% had thyroid function tests and 41% had liver function tests. At 1 year, of those still on treatment, 35% had both liver and thyroid function tests.

Conclusion: Monitoring of thyroid, liver and pulmonary function tests in patients on amiodarone is less than ideal. This is probably because of lack of awareness of current guidelines.
Specificity of the monoclonal antibody 3H8 in the immunohistochemical identification of Candida species
Authors: Järvensivu A , Rautemaa R , Sorsa T , Richardson M
Published: April 2006

Candida albicans has been shown to be involved in the pathogenesis of adult periodontitis (AP). The diagnosis of Candida‐associated AP depends largely on the identification of yeast and pseudomycelial forms in gingival tissue samples by using periodic acid‐Schiff and Gomori methenamine silver stains. However, these stains are non‐specific and also reveal confusing artifacts seemingly rather difficult to distinguish from yeasts. With the recent development and availability of monoclonal antibodies (Mabs) to various epitopes of C. albicans, for example Mab 3H8 which recognizes a mannoprotein, it is now possible to identify Candida in human tissue biopsies. To explore further the usefulness of this Mab in detecting Candida in periodontal disease the antibody was tested against a wide range of yeast species and strains and various morphological forms, grown in agar blocks at various temperatures and for various time periods. Furthermore, considering the location of the 3H8 epitope on the external cell wall of certain C. albicans strains, it seemed reasonable to determine whether the epitope could be expressed into the surrounding environment, further aiding the recognition of the organism in tissue. The 3H8 epitope appeared to be located at the external surface and on the septum between the mother cell and germ tube of some C. albicans strains but it was partially cryptic in the cell wall of other strains. Both yeast blastoconidia and pseudohyphae were labeled by the 3H8 antibody. Candida lusitaniae, C. glabrata, C. krusei, C. parapsilosis and C. tropicalis did not posses the epitope. The epitope was expressed extracellularly by both blastoconidia and pseudohyphae of C. albicans. This Mab appears to be suitable for the identification of C. albicans in periodontal tissue and may provide further insight into the role of C. albicans in the pathogenesis and diagnosis of periodontal diseases.
The vasodepressor function of the kidney: prostaglandin E2 is not the principal vasodepressor lipid of the renal medulla
Authors: Glodny B. , Pauli G. F.
Published: April 2006

Aim:  Whereas prostaglandin E2 has been characterized as the principal vasodepressor lipid, medullipin remains a hypothetical vasodepressor principle of the renal medulla. Representing the first step towards the isolation of medullipin as a pure compound, the aim of the present study was to determine whether or not the known vasodilator and antihypertensive action of prostaglandins play a role in the antihypertensive activity of renal medulla.

Methods:  A chloroform extract of porcine kidney medulla was fractionated by gradient vacuum liquid chromatography (VLC) and analysed by capillary GC‐MS for the presence of prostaglandins (detection limit: 2.2 ppm). The biological activity was determined in spontaneously hypertensive Wistar rats. The particle size of injectable colloids prepared from extract and fractions was controlled by photon correlation spectroscopy.

Results:  The extract caused a pronounced blood pressure decline (29.6 ± 6.3/24.9± 5.5 mmHg; P = 0.0078; 10 mg kg−1 body weight; particle size of 143 ± 18 nm; n = 7) lasting for more than 1 h. The heart rate remained stable, showing only a slightly decrease. All fractions were shown to be devoid of vasodilator prostanoid substances. The VLC procedure allowed the successful separation of endogenous emulsifiers from the active principle. An extract from the renal cortex did not exhibit a similar vasodepressor effect.

Conclusion:  Prostaglandins are excluded as the blood pressure‐lowering active principle of a total lipid kidney medulla extract. The vasodepressor principle is contained in the kidney medulla, but not in the cortex. It can be separated from endogenous emulsifying substances, is chromatographically stable, and is amenable to purification and chemical characterization.
The probability of large deviations for the sum functions of spacings
Authors: Mirakhmedov Sherzod Mira′zam
Published: April 2006

Let 0 = U0,n ≤ U1,n ≤ ⋯≤Un−1,n ≤ Un,n = 1 be an ordered sample from uniform [0, 1] distribution, and Din = Ui,n − Ui−1,n, i = 1, 2, …, n; n = 1, 2, …, be their spacings, and let f1n, …, fnn be a set of measurable functions. In this paper, the probabilities of the
moderate and Cramer‐type large deviation theorems for statistics
Rn(D) = f1n(nD1n) + ⋯+fnn(nDnn) are proved. Application of these theorems for determination of the
intermediate efficiencies of the tests based on Rn(D)‐type statistic is presented here too.
A case study in pathway knowledgebase verification
Authors: Racunas Stephen A , Shah Nigam H , Fedoroff Nina V
Published: April 2006

Background

Biological databases and pathway knowledgebases are proliferating rapidly. We are developing software tools for computer-aided hypothesis design and evaluation, and we would like our tools to take advantage of the information stored in these repositories. But before we can reliably use a pathway knowledgebase as a data source, we need to proofread it to ensure that it can fully support computer-aided information integration and inference.

Results

We design a series of logical tests to detect potential problems we might encounter using a particular knowledgebase, the Reactome database, with a particular computer-aided hypothesis evaluation tool, HyBrow. We develop an explicit formal language from the language implicit in the Reactome data format and specify a logic to evaluate models expressed using this language. We use the formalism of finite model theory in this work. We then use this logic to formulate tests for desirable properties (such as completeness, consistency, and well-formedness) for pathways stored in Reactome.

We apply these tests to the publicly available Reactome releases (releases 10 through 14) and compare the results, which highlight Reactome's steady improvement in terms of decreasing inconsistencies. We also investigate and discuss Reactome's potential for supporting computer-aided inference tools.

Conclusion

The case study described in this work demonstrates that it is possible to use our model theory based approach to identify problems one might encounter using a knowledgebase to support hypothesis evaluation tools. The methodology we use is general and is in no way restricted to the specific knowledgebase employed in this case study. Future application of this methodology will enable us to compare pathway resources with respect to the generic properties such resources will need to possess if they are to support automated reasoning.
Quantitative evaluation of RASSF1Amethylation in the non-lesional, regenerative and neoplastic liver
Authors: Di Gioia Sonia , Bianchi Paolo , Destro Annarita , Grizzi Fabio , Malesci Alberto , Laghi Luigi , Levrero Massimo , Morabito Alberto , Roncalli Massimo
Published: April 2006

Background

Epigenetic changes during ageing and their relationship with cancer are under the focus of intense research. RASSF1A and NORE1A are novel genes acting in concert in the proapoptotic pathway of the RAS signalling. While NORE1A has not been previously investigated in the human liver, recent reports have suggested that RASSF1A is frequently epigenetically methylated not only in HCC but also in the cirrhotic liver.

Methods

To address whether epigenetic changes take place in connection to age and/or to the underlying disease, we investigated RASSF1A and NORE1A gene promoter methylation by conventional methylation specific PCR and Real-Time MSP in a series of hepatitic and non-hepatitic livers harboring regenerative/hyperplastic (cirrhosis/focal nodular hyperplasia), dysplastic (large regenerative, low and high grade dysplastic nodules) and neoplastic (hepatocellular adenoma and carcinoma) growths.

Results

In the hepatitic liver (chronic hepatitic/cirrhosis, hepatocellular nodules and HCC) we found widespread RASSF1A gene promoter methylation with a methylation index that increased from regenerative conditions (cirrhosis) to hepatocellular nodules (p < 0.01) to HCC (p < 0.001). In the non-hepatitic liver a consistent pattern of gene methylation was also found in both lesional (focal nodular hyperplasia and hepatocellular adenoma) and non-lesional tissue. Specifically, hepatocellular adenomas (HA) showed a methylation index significantly higher than that detected in focal nodular hyperplasia (FNH) (p < 0.01) and in non-lesional tissue (p < 0.001). In non-lesional liver also the methylation index gradually increased by ageing (p = 0.002), suggesting a progressive spreading of methylated cells over time. As opposed to RASSF1A gene promoter methylation, NORE1A gene was never found epigenetically alterated in both hepatitic and non-hepatitic liver.

Conclusion

We have shown that in non-lesional, regenerative and neoplastic liver the RASSF1A gene is increasingly methylated, that this condition takes place as an age-related phenomenon and that the early setting and spreading over time of an epigenetically methylated hepatocyte subpopulation, might be related to liver tumorigenesis.
Comparison of age-specific cataract prevalence in two population-based surveys 6 years apart
Authors: Tan Ava Grace , Wang Jie Jin , Rochtchina Elena , Mitchell Paul
Published: April 2006

Background

In this study, we aimed to compare age-specific cortical, nuclear and posterior subcapsular (PSC) cataract prevalence in two surveys 6 years apart.

Methods

The Blue Mountains Eye Study examined 3654 participants (82.4% of those eligible) in cross-section I (1992–4) and 3509 participants (75.1% of survivors and 85.2% of newly eligible) in cross-section II (1997–2000, 66.5% overlap with cross-section I). Cataract was assessed from lens photographs following the Wisconsin Cataract Grading System. Cortical cataract was defined if cortical opacity comprised ≥ 5% of lens area. Nuclear cataract was defined if nuclear opacity ≥ Wisconsin standard 4. PSC was defined if any present. Any cataract was defined to include persons who had previous cataract surgery. Weighted kappa for inter-grader reliability was 0.82, 0.55 and 0.82 for cortical, nuclear and PSC cataract, respectively. We assessed age-specific prevalence using an interval of 5 years, so that participants within each age group were independent between the two surveys.

Results

Age and gender distributions were similar between the two populations. The age-specific prevalence of cortical (23.8% in 1st, 23.7% in 2nd) and PSC cataract (6.3%, 6.0%) was similar. The prevalence of nuclear cataract increased slightly from 18.7% to 23.9%. After age standardization, the similar prevalence of cortical (23.8%, 23.5%) and PSC cataract (6.3%, 5.9%), and the increased prevalence of nuclear cataract (18.7%, 24.2%) remained.

Conclusion

In two surveys of two population-based samples with similar age and gender distributions, we found a relatively stable cortical and PSC cataract prevalence over a 6-year period. The increased prevalence of nuclear cataract deserves further study.
Severe airway stenosis associated with Crohn's disease: Case report
Authors: Plataki Maria , Tzortzaki Eleni , Lambiri Irene , Giannikaki Elpida , Ernst Armin , Siafakas Nikolaos M
Published: April 2006

Background

Symptomatic respiratory tract involvement is not common in Crohn's disease. Upper-airway obstruction has been reported before in Crohn's disease and usually responds well to steroid treatment.

Case presentation

We report a case of a 32-year old patient with Crohn's disease who presented with progressively worsening dyspnea on exertion. Magnetic Resonance Imaging of the chest and bronchoscopy revealed severe tracheal stenosis and marked inflammation of tracheal mucosa. Histopathology of the lesion showed acute and chronic inflammation and extended ulceration of bronchial mucosa, without granulomas. Tracheal stenosis was attributed to Crohn's disease after exclusion of other possible causes and oral and inhaled steroids were administered. Despite steroid treatment, tracheal stenosis persisted and only mild symptomatic improvement was noted after 8 months of therapy. The patient subsequently underwent rigid bronchoscopy with successful dilatation and ablation of the stenosed areas and remission of her symptoms.

Conclusion

Respiratory involvement in Crohn's disease might be more common than appreciated. Interventional pulmonology techniques should be considered in cases of tracheal stenosis due to Crohn's disease refractory to steroid treatment.
Performances and microbial features of an aerobic packed-bed biofilm reactor developed to post-treat an olive mill effluent from an anaerobic GAC reactor
Authors: Bertin Lorenzo , Colao Maria Chiara , Ruzzi Maurizio , Marchetti Leonardo , Fava Fabio
Published: April 2006

Background

Olive mill wastewater (OMW) is the aqueous effluent of olive oil producing processes. Given its high COD and content of phenols, it has to be decontaminated before being discharged. Anaerobic digestion is one of the most promising treatment process for such an effluent, as it combines high decontamination efficiency with methane production. The large scale anaerobic digestion of OMWs is normally conducted in dispersed-growth reactors, where however are generally achieved unsatisfactory COD removal and methane production yields. The possibility of intensifying the performance of the process using a packed bed biofilm reactor, as anaerobic treatment alternative, was demonstrated. Even in this case, however, a post-treatment step is required to further reduce the COD. In this work, a biological post-treatment, consisting of an aerobic biological "Manville" silica bead-packed bed aerobic reactor, was developed, tested for its ability to complete COD removal from the anaerobic digestion effluents, and characterized biologically through molecular tools.

Results

The aerobic post-treatment was assessed through a 2 month-continuous feeding with the digested effluent at 50.42 and 2.04 gl-1day-1of COD and phenol loading rates, respectively. It was found to be a stable process, able to remove 24 and 39% of such organic loads, respectively, and to account for 1/4 of the overall decontamination efficiency displayed by the anaerobic-aerobic integrated system when fed with an amended OMW at 31.74 and 1.70 gl-1day-1of COD and phenol loading rates, respectively. Analysis of 16S rRNA gene sequences of biomass samples from the aerobic reactor biofilm revealed that it was colonized byRhodobacterales,Bacteroidales,Pseudomonadales,Enterobacteriales,Rhodocyclalesand genera incertae sedis TM7. Some taxons occurring in the influent were not detected in the biofilm, whereas others, such asParacoccus,Pseudomonas, AcinetobacterandEnterobacter, enriched significantly in the biofilter throughout the treatment.

Conclusion

The silica-bead packed bed biofilm reactor developed and characterized in this study was able to significantly decontaminate anaerobically digested OMWs. Therefore, the application of an integrated anaerobic-aerobic process resulted in an improved system for valorization and decontamination of OMWs.
Do visual analogue scale (VAS) derived standard gamble (SG) utilities agree with Health Utilities Index utilities? A comparison of patient and community preferences for health status in rheumatoid arthritis patients
Authors: Rashidi Amir Adel , Anis Aslam H , Marra Carlo A
Published: April 2006

Background

Assessment of Health Related Quality of Life (HRQL) has become increasingly important and various direct and indirect methods and instruments have been devised to measure it. In direct methods such as Visual Analog Scale (VAS) and Standard Gamble (SG), respondent both assesses and values health states therefore the final score reflects patient's preferences. In indirect methods such as multi-attribute health status classification systems, the patient provides the assessment of a health state and then a multi-attribute utility function is used for evaluation of the health state. Because these functions have been estimated using valuations of general population, the final score reflects community's preferences. The objective of this study is to assess the agreement between community preferences derived from the Health Utilities Index Mark 2 (HUI2) and Mark 3 (HUI3) systems, and patient preferences.

Methods

Visual analog scale (VAS) and HUI scores were obtained from a sample of 320 rheumatoid arthritis patients. VAS scores were adjusted for end-aversion bias and transformed to standard gamble (SG) utility scores using 8 different power conversion formulas reported in other studies. Individual level agreement between SG utilities and HUI2 and HUI3 utilities was assessed using the intraclass correlation coefficient (ICC). Group level agreement was assessed by comparing group means using the paired t-test.

Results

After examining all 8 different SG estimates, the ICC (95% confidence interval) between SG and HUI2 utilities ranged from 0.45 (0.36 to 0.54) to 0.55 (0.47 to 0.62). The ICC between SG and HUI3 utilities ranged from 0.45 (0.35 to 0.53) to 0.57 (0.49 to 0.64). The mean differences between SG and HUI2 utilities ranged from 0.10 (0.08 to 0.12) to 0.22 (0.20 to 0.24). The mean differences between SG and HUI3 utilities ranged from 0.18 (0.16 to 0.2) to 0.28 (0.26 to 0.3).

Conclusion

At the individual level, patient and community preferences show moderate to strong agreement, but at the group level they have clinically important and statistically significant differences. Using different sources of preference might alter clinical and policy decisions that are based on methods that incorporate HRQL assessment. VAS-derived utility scores are not good substitutes for HUI scores.
A method for the generation of standardized qualitative dynamical systems of regulatory networks
Authors: Mendoza Luis , Xenarios Ioannis
Published: April 2006

Background

Modeling of molecular networks is necessary to understand their dynamical properties. While a wealth of information on molecular connectivity is available, there are still relatively few data regarding the precise stoichiometry and kinetics of the biochemical reactions underlying most molecular networks. This imbalance has limited the development of dynamical models of biological networks to a small number of well-characterized systems. To overcome this problem, we wanted to develop a methodology that would systematically create dynamical models of regulatory networks where the flow of information is known but the biochemical reactions are not. There are already diverse methodologies for modeling regulatory networks, but we aimed to create a method that could be completely standardized,i.e.independent of the network under study, so as to use it systematically.

Results

We developed a set of equations that can be used to translate the graph of any regulatory network into a continuous dynamical system. Furthermore, it is also possible to locate its stable steady states. The method is based on the construction of two dynamical systems for a given network, one discrete and one continuous. The stable steady states of the discrete system can be found analytically, so they are used to locate the stable steady states of the continuous system numerically. To provide an example of the applicability of the method, we used it to model the regulatory network controlling T helper cell differentiation.

Conclusion

The proposed equations have a form that permit any regulatory network to be translated into a continuous dynamical system, and also find its steady stable states. We showed that by applying the method to the T helper regulatory network it is possible to find its known states of activation, which correspond the molecular profiles observed in the precursor and effector cell types.
Antibiotic resistance as a global threat: Evidence from China, Kuwait and the United States
Authors: Zhang Ruifang , Eggleston Karen , Rotimi Vincent , Zeckhauser Richard J
Published: April 2006

Background

Antimicrobial resistance is an under-appreciated threat to public health in nations around the globe. With globalization booming, it is important to understand international patterns of resistance. If countries already experience similar patterns of resistance, it may be too late to worry about international spread. If large countries or groups of countries that are likely to leap ahead in their integration with the rest of the world – China being the standout case – have high and distinctive patterns of resistance, then a coordinated response could substantially help to control the spread of resistance. The literature to date provides only limited evidence on these issues.

Methods

We study the recent patterns of antibiotic resistance in three geographically separated, and culturally and economically distinct countries – China, Kuwait and the United States – to gauge the range and depth of this global health threat, and its potential for growth as globalization expands. Our primary measures are the prevalence of resistance of specific bacteria to specific antibiotics. We also propose and illustrate methods for aggregating specific "bug-drug" data. We use these aggregate measures to summarize the resistance pattern for each country and to study the extent of correlation between countries' patterns of drug resistance.

Results

We find that China has the highest level of antibiotic resistance, followed by Kuwait and the U.S. In a study of resistance patterns of several most common bacteria in China in 1999 and 2001, the mean prevalence of resistance among hospital-acquired infections was as high as 41% (with a range from 23% to 77%) and that among community- acquired infections was 26% (with a range from 15% to 39%). China also has the most rapid growth rate of resistance (22% average growth in a study spanning 1994 to 2000). Kuwait is second (17% average growth in a period from 1999 to 2003), and the U.S. the lowest (6% from 1999 to 2002). Patterns of resistance across the three countries are not highly correlated; the most correlated were China and Kuwait, followed by Kuwait and the U.S., and the least correlated pair was China and the U.S.

Conclusion

Antimicrobial resistance is a serious and growing problem in all three countries. To date, there is not strong international convergence in the countries' resistance patterns. This finding may change with the greater international travel that will accompany globalization. Future research on the determinants of drug resistance patterns, and their international convergence or divergence, should be a priority.
Finnish Bomb Threats: Offence and Offender Characteristics
Authors: Häkkänen Helinä
Published: April 2006

The current explorative study explored the offence and offender characteristics in Finnish bomb threats (N = 69). The results showed that the bomb threats were most frequently targeted at restaurants and shopping centres. The offenders almost exclusively used telephones in communicating their threats. Most frequently, it was their own, recognisable phone number. The bomb threats were usually direct and contained very little information. In 29% of the cases, the offender had been at the target location within 24 hours of the bomb threat. The results showed further that a typical person making the bomb threat was a middle-aged man with a criminal background, who works at a construction site. The most frequent motive for making the threat was revenge or vandalism. The results also indicated that the offender characteristics cannot be reliably inferred by assessing the target or the threat. The findings are discussed with regard to the previous research on bomb-related offences.