bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using Approximate Bayesian Computation to Estimate Tuberculosis Transmission Parameters From Genotype Data
Authors: Tanaka Mark M , Francis Andrew R , Luciani Fabio , Sisson S A 
Published: April 2006

Abstract
Tuberculosis can be studied at the population level by genotyping strains of Mycobacterium tuberculosis isolated from patients. We use an approximate Bayesian computational method in combination with a stochastic model of tuberculosis transmission and mutation of a molecular marker to estimate the net transmission rate, the doubling time, and the reproductive value of the pathogen. This method is applied to a published data set from San Francisco of tuberculosis genotypes based on the marker IS6110. The mutation rate of this marker has previously been studied, and we use those estimates to form a prior distribution of mutation rates in the inference procedure. The posterior point estimates of the key parameters of interest for these data are as follows: net transmission rate, 0.69/year [95% credibility interval (C.I.) 0.38, 1.08]; doubling time, 1.08 years (95% C.I. 0.64, 1.82); and reproductive value 3.4 (95% C.I. 1.4, 79.7). These figures suggest a rapidly spreading epidemic, consistent with observations of the resurgence of tuberculosis in the United States in the 1980s and 1990s.
A Simple Linear Regression Method for Quantitative Trait Loci Linkage Analysis With Censored Observations
Authors: Anderson Carl A , McRae Allan F , Visscher Peter M 
Published: April 2006

AbstractStandard quantitative trait loci (QTL) mapping techniques commonly assume that the trait is both fully observed and normally distributed. When considering survival or age-at-onset traits these assumptions are often incorrect. Methods have been developed to map QTL for survival traits; however, they are both computationally intensive and not available in standard genome analysis software packages. We propose a grouped linear regression method for the analysis of continuous survival data. Using simulation we compare this method to both the Cox and Weibull proportional hazards models and a standard linear regression method that ignores censoring. The grouped linear regression method is of equivalent power to both the Cox and Weibull proportional hazards methods and is significantly better than the standard linear regression method when censored observations are present. The method is also robust to the proportion of censored individuals and the underlying distribution of the trait. On the basis of linear regression methodology, the grouped linear regression model is computationally simple and fast and can be implemented readily in freely available statistical software.
Definition of a 1.06-Mb Region Linked to Neuroinflammation in Humans, Rats and Mice
Authors: Öckinger Johan , Serrano-Fernández Pablo , Möller Steffen , Ibrahim Saleh M , Olsson Tomas , Jagodic Maja 
Published: April 2006

AbstractUnbiased identification of susceptibility genes might provide new insights into pathogenic mechanisms that govern complex inflammatory diseases such as multiple sclerosis. In this study we fine mapped Eae18a, a region on rat chromosome 10 that regulates experimental autoimmune encephalomyelitis (EAE), an animal model for multiple sclerosis. We utilized two independent approaches: (1) in silico mapping based on sequence similarity between human multiple sclerosis susceptibility regions and rodent EAE quantitative trait loci and (2) linkage mapping in an F10 (DA × PVG.AV1) rat advanced intercrossed line. The linkage mapping defines Eae18a to a 5-Mb region, which overlaps one intergenomic consensus region identified in silico. The combined approach confirms experimentally, for the first time, the accuracy of the in silico method. Moreover, the shared intersection between the results of both mapping techniques defines a 1.06-Mb region containing 13 candidate genes for the regulation of neuroinflammation in humans, rats, and mice.
‘Per il bene di … nostra cipta’: Borso d'Este and the Certosa of Ferrara*
Authors: Rosenberg Charles M. 
Published: April 2006

Although the Este family had traditionally supported numerous monastic foundations, Borso d'Este's patronage of the Carthusian order is notable in that it introduced a new religious community into Ferrara. The history of the establishment, development, and decoration of the Charterhouse of Ferrara is indicative of the taste, artistic and religious views, and political exigencies which shaped the religious patronage of Borso d'Este, Duke of Ferrara, Modena, and Reggio. At the same time, the specific examples of Borso's monastic patronage are illustrative of the fundamental assumptions underlying fifteenth-century aristocratic support of religious foundations.On April 23,1452, Borso d'Este laid the cornerstone for the Certosa on a site not far from the Este villa of Belfiore and the Dominican Monastery of Santa Maria degli Angeli. By spring 1461, the Monastery was habitable, though not yet complete.
Azide–Tetrazole Ring‐Chain Isomerism in Polyazido‐1,3,5‐triazines, Triazido‐s‐heptazine, and Diazidotetrazines
Authors: Hammerl Anton , Klapötke Thomas M. , Rocha Reginaldo 
Published: April 2006

AbstractThe azide–tetrazole isomerism in several polyazido‐1,3,5‐triazines, triazido‐sym‐heptazine, and some diazido‐1,2,4,5‐tetrazines was investigated by ab initio quantum chemical methods in order to determine whether the polyazides are suitable starting materials for the synthesis of the isomeric tetrazoles. The effects of solvation in CCl4, DMSO and water on this isomerism were included using the self consistent reaction field (SCRF) method. The effect of amino‐ and nitrosubstituents on the azide–tetrazole isomerism was also examined. In the gas phase all investigated polyazidoheterocycles do not cyclize to form tetrazoles. An electron‐donating amino group favors the ring closure to tetrazoles, whereas an electron‐withdrawing nitro group favors the azides. Solvation in polar solvents favors the formation of a tetrazole ring system due to higher charge separation in the tetrazole ring system, but for all polyazido‐1,3,5‐triazines, including triazido‐s‐heptazine, the effects of solvation are not strong enough to shift the equilibrium to the tetrazole side, which explains why several attempts to detect these compounds have failed. The monotetetrazoles of diazidotetrazine and bis(azido)azo‐1,2,4,5‐tetrazine and the ditetrazole of bis(azido)hydrazo‐1,2,4,5‐tetrazine are the minimum energy species in DMSO and water. Thus we predict that the diazidoazo‐ and hydrazotetrazines will readily cyclize to the tetrazoles in polar solvents. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Site‐specific delivery of dexamethasone from biodegradable implants reduces formation of pericardial adhesions in rabbits
Authors: Chorny Michael , Mishaly David , Leibowitz Avshalom , Domb Abraham J. , Golomb Gershon 
Published: April 2006

AbstractRepeated sternotomy often leads to serious complications in patients due to the formation of cardiac adhesions. In this study we characterized dexamethasone‐loaded biodegradable poly(lactide)‐poly(ethyleneglycol) copolymer films for site‐specific drug delivery and examined their efficacy in the rabbit model of postoperative cardiac adhesions. Tritiated dexamethasone‐loaded films were used to determine the in vitro release and in vivo drug distribution. Dexamethasone release in serum was biphasic with 69% drug released after 72 hr. The implants produced sustained drug levels at the implantation site with low distribution into the peripheral tissues. The matrices were implanted in rabbits between the epicardium and the sternum following sternotomy, pericardiectomy and epicardium abrasion, with the drug‐releasing surface facing the epicardium. The tenacity and density of the adhesions was examined 21 days post procedure in comparison to both groups of untreated and rabbits implanted with blank matrices. Similarly tenacious and dense adhesions were observed in both control groups. In contrast, epicardial adhesions' formation was significantly reduced and the anatomy was preserved in the treated animals. It is concluded that local delivery of dexamethasone from biodegradable implants provides a promising approach for the prevention of pericardial adhesions while potentially minimizing the systemic adverse effects inherent to systemic therapy or high blood levels of the drug. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res, 2006
Toxoplasma gondii, HCV, and HBV seroprevalence and co‐infection among HIV‐positive and ‐negative pregnant women in Burkina Faso
Authors: Simpore Jacques , Savadogo Aly , Ilboudo Denise , Nadambega Marie Christelle , Esposito Maria , Yara Justine , Pignatelli Salvatore , Pietra Virginio , Musumeci Salvatore 
Published: April 2006

AbstractToxoplasma gondii (T. gondii) infections can cause serious complications in HIV‐infected pregnant women, leading to miscarriage, stillbirth, birth defects (e.g., mental retardation, blindness, epilepsy etc.) and could favor or enhance the mother‐to‐child transmission of HCV, HBV, and HIV vertical transmission. From May 20, 2004 to August 3, 2005, 336 18–45 years aged pregnant women, were enrolled for an investigation of the prevalence of serum antibodies against T. gondii, HCV, HBV, and HIV using ELISA. The prevalence of T. gondii, HCV, and HBV in pregnant women was 25.3%, 5.4%, and 9.8%, respectively and the HIV serostatus (61.6%) seems to be associated with greater prevalence rates of both T. gondii (28.5% vs. 20.2%) and HBV (11.6% vs. 7.0%). Without taking into account HIV, only 65.5% (220 of 336) of the women were not infected with these agents. The co‐infection rate between HIV‐infected and ‐negative women was different statistically: T. gondii/HBV 0.048 versus 0.015, T. gondii/HCV 0.014 versus 0.008, and HCV/HBV 0.005 versus 0.008, respectively. The elevated co‐infection rate in HIV‐positive women demonstrated that they are exposed to T. gondii, HCV, and HBV infections prevalently by sexual contact. J. Med. Virol. 78:730–733, 2006. © 2006 Wiley‐Liss, Inc.
The epimerization of peptide aldehydes—a systematic study
Authors: Ganneau Cécile , Moulin Aline , Demange Luc , Martinez Jean , Fehrentz Jean‐Alain 
Published: April 2006

AbstractPeptide aldehydes are interesting targets as enzyme inhibitors, and can be used for pseudopeptide chemistry or ligation. However, they are known to be subjected to epimerization during synthesis or purification. By 1H NMR, a model dipeptide aldehyde can be used to check the possible epimerization occurring during synthesis. Various purification methods were investigated, but none was free from epimerization. Copyright © 2006 European Peptide Society and John Wiley & Sons, Ltd.
Similarity of steady stratified flows
Authors: Yih Chia-Shun 
Published: April 2006

Steady flows of an incompressible, inviscid, and non-diffusive fluid of variable density in a gravitational field are first considered. By a transformation it is shown conclusively that there are infinitely many flows with the same flow pattern, provided the density gradients of these flows at any section (e.g. far upstream) differ only by a multiplicative constant. These flows have identical local internal Froude numbers at all corresponding points of the flows and, hence, identical local Richardson numbers. They are therefore dynamically similar. Every time a solution for one stratification is obtained, one has in fact obtained the solutions for infinitely many stratifications.The creation of vorticity in steady stratified flows is then examined, and it is shown that this creation can be divided into two parts, one part being entirely due to the inertial effect and the other originating from the gravity effect of density variation.Finally, compressibility is considered and the results on similarity of stratified flows and on vorticity and circulation are extended to apply to steady flows of gases stratified in entropy.
Theory of the pressure–strain rate. Part 2. Diagonal elements
Authors: Weinstock J. 
Published: April 2006

A theoretical calculation is made of (the diagonal elements of) pressure-strain-rate calculation ρ0−1〈p[∇u + (∇u)T]〉 for a simple turbulent shear flow. This calculation parallels a previous calculation of the off-diagonal element. The calculation is described as follows. (1) Beginning with the Navier-Stokes equation, an expression for the (diagonal) pressure-strain-rate term is derived analytically in terms of measurable quantities (velocity spectra) - this derivation makes use of a cumulant discard. (2) It is proved that, to lowest order in the spectral anisotropy, the diagonal pressure-strain-rate term is linearly proportional to the diagonal Reynolds-stress elements. (3) A formula is derived for the proportionality constants (Rotta constants) in terms of arbitrary spectra. (4) This formula is used to calculate theoretically the numerical value of Rotta's constant Cii for models of velocity spectra (the variation of Cii with variations of spectral shapes and of Reynolds number are also determined). (5) Deficiencies and limitations of Rotta's model are identified and discussed.It is found that Rotta's expression for 2ρ0−1〈p∂ui/∂i〉 is only valid for special spectra. Surprisingly large deviations of Rotta's expression from theory are found for a more complex spectra thought to be typical of simple shear flow. In addition, it is found that Cxz is intrinsically and quantitatively different from Cii because the latter depends importantly on the large-wavenumber part of the spectrum (the inertial subrange) whereas the former does not. The numerical ratio Czz/Cxz is calculated theoretically and shown to be about 2 for the zero-moment model. It is concluded that a linear term in the stress anisotropy as proposed by Rotta does not always exist. The deviation of Rotta's model from theory is understood by distinguishing between the spectral anisotropy and the stress anisotropy.For the zero-moment spectral model, where the Rotta relation is valid, it is found that Cii varies significantly with large Reynolds number but is rather insensitive to the large-wavelength part of the spectrum.
High-strain-rate free-surface boundary-layer flows
Authors: Bertschy J. R. , Chin R. W. , Abernathy F. H. 
Published: April 2006

Two-dimensional boundary-layer flows of water down an inclined table were investigated in both the laminar and turbulent regimes. Mean, r.m.s. and skewness and velocity spectra were determined from streamwise velocity measurements. Two laser-Doppler anemometry methods were developed (for studying polymer-solution flows using this same water table) and compared with measurements obtained using hot-film anemometry. All three techniques obtained consistent results.An analysis based on a von Mises transformation is presented which accurately predicts the mean-velocity profile and flow development in the laminar regime. High strain rates are achieved which can be varied independently of Reynolds number, and turbulent flows are easily generated by inserting a disturbance. These turbulent flows are surprisingly similar to more commonly investigated turbulent boundarylayer flows of much greater y+ extent. Turbulent water-table flows typically extend only to y+ = 100, yet mean velocity essentially follows the law of the wall, and intensity and skewness measurements are similar to those obtained in flows much less limited in y+.
The production of turbulent stress in a shear flow by irrotational fluctuations
Authors: Gartshore I. S. , Durbin P. A. , Hunt J. C. R. 
Published: April 2006

This paper is a study of how external turbulence affects an initially turbulence-free region in which there is a mean-velocity gradient dU/dz. Rapid-distortion theory shows how external turbulence induces irrotational fluctuations in the sheared region, which interact with the shear to produce rotational velocity fluctuations and mean Reynolds stresses. These stresses extend into the sheared region over a distance of the order of the integral scale L∞. Since the actual front between the initial external turbulence and the shear flow is a randomly contorted surface, the turbulence of a fixed point near the front is intermittent. Intermittency is included in the present analysis by a simple statistical model.Experiments were done in a wind tunnel with the flow divided by a plate extending from upstream to x = 0. Above the plate, turbulence was produced by a grid. Below the plate a low turbulence shear was produced by wire screens. The wake of the plate (x > 0) decayed downstream.Turbulent shear stress was observed to grow from zero to significant values in the interaction region. The magnitude and extent of the observed stress agrees reasonably well with predictions. We conclude that turbulent stresses can be produced by irrotational fluctuations in a region of mean shear, and that this effect can be estimated using rapid-distortion theory.
Oscillatory convection in vertical slots
Authors: Koster J. N. , MÜLler U. 
Published: April 2006

Convective flow phenomena in slender vertical slots with larger vertical than horizontal dimension, i.e. Hele Shaw slots, heated from below and subject to specified lateral boundary conditions, are investigated experimentally. Temperature fields in the liquid were visualized by holographic interferometry. Power-density spectra of local time-dependent thermocouple signals are calculated.In these slender slots different steady and time-dependent convection patterns develop with increasing Rayleigh number. The range of oscillatory convective flow exhibits periodic, quasiperiodic or non-periodic structures including possible frequency locking, subharmonics and intermittency. Quasiperiodic and periodic oscillations reappear at higher Rayleigh numbers, with non-periodic flows occurring in-between. These time-dependent flows appear to be caused by an instability of thermal boundary layers at the horizontal walls. Finally, at still higher Rayleigh numbers a reverse transition to a steady-state flow pattern is observed. The transitions between steady and non-steady flows are characterized by hysteresis.
A steady-unsteady visualization technique for wake-flow studies
Authors: Ilegbusi J. O. , Spalding D. B. 
Published: April 2006

A description is given of the principle and a preliminary embodiment of a flow-visualization technique in which the test body is pulled through water.Initially, dyed and undyed parts of the water are separated by a plane horizontal interface; as the body emerges from below this interface, it carries dyed fluid upwards in its wake. A succession of photographs reveals the nature of the flow.In principle, the flow is steady in a frame fixed relative to the body, and unsteady in one relative to the tank and the initial interface. Interpretation of the experimental results must therefore proceed by way of an analysis in which the steady-state equations are solved for velocity and turbulence quantities but an unsteady-state equation is solved for the dye concentration.Preliminary results are reported for the flows behind a wedge and behind a bar. They reveal that these particular flows are unsteady even in the body-fixed coordinate frame, being strongly oscillatory.
Self-sustained radial oscillating flows between parallel disks
Authors: Mochizuki S. , Yang Wen-Jei 
Published: April 2006

The flow-visualization methods of dye injection, hydrogen-bubble generation and paraffin mist are employed to investigate radial flow between parallel circular disks with a steady influx. Three distinct flow patterns are observed in the range of Re between 1.5 and 50. (1) Steady flow without boundary-layer separation and re-attachment, for Re < Rec. (2) A self-controlled flow oscillation which decays further downstream, in the range of Rec [les ] Re < Ret. (3) A self-sustained flow fluctuation which develops into a laminar-turbulent transition with a reverse transition further downstream, when Re [ges ] Ret. Rec and Ret are the critical and transition Reynolds number, respectively.The oscillating flows are caused by a vortex street consisting of vortices (i.e. separating annular bubbles) that separate periodically and alternately from both disks. Finite-difference solutions of the unsteady vorticity transport equation broadly agree with certain experimental observations. The study concludes that the separation and reattachment of shear layers in the radial flow through parallel disks are unsteady phenomena and the sequence of nucleation, growth, migration and decay of the vortices is self-sustained.
Structure of large-scale vortices and unsteady reverse flow in the reattaching zone of a turbulent separation bubble
Authors: Kiya Masaru , Sasaki Kyuro 
Published: April 2006

This paper describes experiments concerning the structure of large-scale vortices and the unsteady reverse-flow properties in the reattaching zone of a nominally two-dimensional separation bubble formed at the leading edge of a blunt flat plate with right-angled corners. The experiment was performed in a wind tunnel with a constant Reynolds number 2.6 × 104 (based on the main-flow velocity and the thickness of the plate). Split-film probes, being sensitive to instantaneous reversals of flow direction, were extensively employed. An important feature of this study is a judicious use of surface-pressure fluctuations as a conditioning signal to educe the structure of the large-scale vortices.Distributions of fluctuating-velocity vectors and contour lines of high-frequency turbulent energy in a few space–time domains are presented and discussed. The most economical interpretation of these space-time distributions is that the large-scale vortices in the reattaching zone are hairpin vortices whose configuration is sketched in the text. The unsteady flow in the reattaching zone is mainly governed by two agents; the motion of the large-scale vortices and the low-frequency unsteadiness. The unsteady flow is clarified in terms of the motion (in a space–time domain) of zeros of the longitudinal velocity close to the surface of the plate; the effects of the two agents on this motion are presented separately. On the basis of these results, a mathematical model of the unsteady flow in the reattaching zone is suggested and found to yield good comparison with measured reverse-flow intermittency and frequency of local-flow reversals. It appears that the separation bubble experiences shrinkage and enlargement in connection with the low-frequency unsteadiness and that the speed of shrinkage is much greater than that of enlargement. The strength of the large-scale vortices in the reattaching zone seems to be dependent on the phase of the low-frequency unsteadiness.