bluuebunny/crossref_metadata_2025_split huggingface dataset:
The dynamics of thin liquid jets in air
Authors: Entov V. M. , Yarin A. L. 
Published: April 2006

The dynamics of propagation and disintegration of laminar liquid jets moving in air has been investigated theoretically. It is assumed that the jet is thin, i.e. the ratio of the characteristic transverse size to the longitudinal one is small. It is assumed also that the lateral surface of the jet is free of shearing forces and is ‘almost free’ of normal ones in the sense that the normal tractions other than isotropic pressure are small in comparison with the internal stresses acting in the jet cross-section.Asymptotic quasi-one-dimensional equations of the continuity, momentum and moment of momentum of liquid motion in the jet have been derived. These equations were used as a basis for studying the process of growth of long-wave bending (transverse) disturbances of high-velocity jets of circular cross-section during their motion through air. The instability condition has been obtained and the growth rate of small bending disturbances of the jet has been found; the evolution of the jet shape at the stage of finite disturbances is investigated.
Stirring and transport of tracer fields by geostrophic turbulence
Authors: Holloway Greg , Kristmannsson Stefan S. 
Published: April 2006

We investigate the interaction of concentration fields of passive tracer with velocity fields characterizing geostrophic turbulence. We develop and compare results from equilibrium statistical mechanics, from turbulence-closure theory and from numerical simulation. A consistent account emerges. Among the results we show (1) that velocity fields efficiently scatter tracer variance to all scales, (2) that tracer variance evolves toward an equilibrium spectrum which is different from the equilibrium spectrum for vorticity variance, and (3) that intermittency of the tracer field is characteristic of a cascade of tracer variance across wavenumber space. The greater efficiency of the cascade of tracer variance relative to a vorticity cascade is due to wavenumber-local advective terms which affect tracer but not vorticity. We suggest that the more efficient tracer cascade results in shorter Lagrangian autocorrelation times for tracer than for vorticity.We investigate the spatial flux of tracer when a uniform gradient of average tracer concentration is imposed. We show (1) that the spatial flux has dominant contributions from fluctuations on scales slightly larger than the dominant energetic scales, (2) that an effective eddy-diffusivity formulation is valid and that the diffusivity agrees with simple mixing-length estimates, and (3) that eddy diffusivity is significantly anisotropic if Rossby-wave propagation occurs. Meridional diffusivity is suppressed relative to zonal diffusivity.We complement the study of stirring down from a uniform gradient with a numerical investigation of the stirring out of an initially concentrated spot. We see that eddy diffusivity can be a dangerous concept for such problems.
Non-uniqueness and stability of the configuration of flow of immiscible fluids with different viscosities
Authors: Joseph D. D. , Nguyen K. , Beavers G. S. 
Published: April 2006

High-viscosity liquids hate to work. Low-viscosity liquids are the victims of the laziness of high-viscosity liquids because they are easy to push around.The arrangement of components in steady flow of immiscible liquids is typically non-unique. The problem of selection of arrangements is defined here and is studied by variational methods under the hypothesis that the realized arrangements are the ones that maximize the speed on exterior boundaries for prescribed boundary tractions, or the ones that minimize the tractions for prescribed speeds. The arrangements which minimize tractions also minimize the dissipation by putting low-viscosity liquid in regions of high shear. The variational problem is used as a guide to intuition in the design and interpretation of experiments when results of analysis of stability are unavailable. In fact we always observe some kind of shielding of high-viscosity liquid. This can occur by sheet coating in which low-viscosity liquid encapsulates high-viscosity liquid, or through the formation of rigidly rotating masses of high-viscosity liquid which we call rollers. In other cases we get emulsions of low-viscosity liquid in a high-viscosity foam. The emulsions arise from a fingering instability. The low-viscosity liquid fingers into the high-viscosity liquid and then low-viscosity bubbles are pinched off the fingers. The emulsions seem to have a very low effective viscosity and they shield the high-viscosity liquid from shearing. In the problem of Taylor instability with two fluids, low-viscosity Taylor cells are separated by stable high-viscosity rollers.
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

SummaryThe 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

SummaryThe 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, 2006Abstract: 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

AbstractAim: 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

AbstractAim:  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.
A case study in pathway knowledgebase verification
Authors: Racunas Stephen A , Shah Nigam H , Fedoroff Nina V 
Published: April 2006

Abstract

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

Abstract

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.