tlCell: a software transactional memory for the cell broadband engine architecture

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do Grau de Mestre em Engenharia Informática

Enamel matrix protein adsorption to root surfaces in the presence or absence of human blood

Background: The clinical use of an enamel matrix derivative (EMD) has been shown to promote formation of new cementum, periodontal ligament (PDL), and bone and to significantly enhance the clinical outcomes after regenerative periodontal surgery. It is currently unknown to what extent the bleeding during periodontal surgery may compete with EMD adsorption to root surfaces. The aim of this study is to evaluate the effect of blood interactions on EMD adsorption to root surfaces mimicking various clinical settings and to test their ability to influence human PDL cell attachment and proliferation. Methods: Teeth extracted for orthodontic reasons were subjected to ex vivo scaling and root planing and treated with 24% EDTA, EMD, and/or human blood in six clinically related settings to determine the ability of EMD to adsorb to root surfaces. Surfaces were analyzed for protein adsorption via scanning electron microscopy and immunohistochemical staining with an anti-EMD antibody. Primary human PDL cells were seeded on root surfaces and quantified for cell attachment and cell proliferation. Results: Plasma proteins from blood samples altered the ability of EMD to adsorb to root surfaces on human teeth. Samples coated with EMD lacking blood demonstrated a consistent even layer of EMD adsorption to the root surface. In vitro experiments with PDL cells demonstrated improved cell attachment and proliferation in all samples coated with EMD (irrespective of EDTA) when compared to samples containing human blood. Conclusion: Based on these findings, it is advised to minimize blood interactions during periodontal surgeries to allow better adsorption of EMD to root surfaces.

Self-consistent resonance absorption with two layer profile steepening

Resonance absorption of p-polarized light, incident at angle 6 on a flowing, stratified plasma, is analyzed; profile steepening within (i) a layer around the turning point, and (ii) a thinner,embedded sublayer at the critical surface is taken into account self-consistently. The entire steepened region is taken as collisionless and isothermal. The structure of the main layer shows a variety of regimes, depending on how the flow crosses a sonic point. The structure of the sublayer is also determined; it is entirely subsonic (with no wave breaking) for a well-defined,broad parameter range. Density changes across both layer and sublayer, and fractional absorption, are given in terms of [(wavelength)2 Xintensity/temperature], and (temperature/mec2). The flow outside the double structure is also analyzed for particular conditions.

Algorithms for efficient transaction management and consistent queries in client -server semantic object-oriented parallel databases

Large read-only or read-write transactions with a large read set and a small write set constitute an important class of transactions used in such applications as data mining, data warehousing, statistical applications, and report generators. Such transactions are best supported with optimistic concurrency, because locking of large amounts of data for extended periods of time is not an acceptable solution. The abort rate in regular optimistic concurrency algorithms increases exponentially with the size of the transaction. The algorithm proposed in this dissertation solves this problem by using a new transaction scheduling technique that allows a large transaction to commit safely with significantly greater probability that can exceed several orders of magnitude versus regular optimistic concurrency algorithms. A performance simulation study and a formal proof of serializability and external consistency of the proposed algorithm are also presented.^ This dissertation also proposes a new query optimization technique (lazy queries). Lazy Queries is an adaptive query execution scheme which optimizes itself as the query runs. Lazy queries can be used to find an intersection of sub-queries in a very efficient way, which does not require full execution of large sub-queries nor does it require any statistical knowledge about the data.^ An efficient optimistic concurrency control algorithm used in a massively parallel B-tree with variable-length keys is introduced. B-trees with variable-length keys can be effectively used in a variety of database types. In particular, we show how such a B-tree was used in our implementation of a semantic object-oriented DBMS. The concurrency control algorithm uses semantically safe optimistic virtual "locks" that achieve very fine granularity in conflict detection. This algorithm ensures serializability and external consistency by using logical clocks and backward validation of transactional queries. A formal proof of correctness of the proposed algorithm is also presented. ^

Numerical modelling of single-layer folding: clarification of an issue regarding the possible effect of computer codes and the influence of initial irregularities

The influence of initial perturbation geometry and material propel-ties on final fold geometry has been investigated using finite-difference (FLAC) and finite-element (MARC) numerical models. Previous studies using these two different codes reported very different folding behaviour although the material properties, boundary conditions and initial perturbation geometries were similar. The current results establish that the discrepancy was not due to the different computer codes but due to the different strain rates employed in the two previous studies (i.e. 10(-6) s(-1) in the FLAC models and 10(-14) s(-1) in the MARC models). As a result, different parts of the elasto-viscous rheological field were bring investigated. For the same material properties, strain rate and boundary conditions, the present results using the two different codes are consistent. A transition in Folding behaviour, from a situation where the geometry of initial perturbation determines final fold shape to a situation where material properties control the final geometry, is produced using both models. This transition takes place with increasing strain rate, decreasing elastic moduli or increasing viscosity (reflecting in each case the increasing influence of the elastic component in the Maxwell elastoviscous rheology). The transition described here is mechanically feasible but is associated with very high stresses in the competent layer (on the order of GPa), which is improbable under natural conditions. (C) 2000 Elsevier Science Ltd. All rights reserved.

Consistent state software transactional memory

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do Grau de Mestre em Engenharia Informática

Ultrastructural and molecular analysis of Bowman's layer corneal dystrophies: an epithelial origin?

PURPOSE: Two mutations (R555Q and R124L) in the BIGH3 gene have been described in anterior or Bowman's layer dystrophies (CDB). The clinical, molecular, and ultrastructural findings of five families with CDB was reviewed to determine whether there is a consistent genotype:phenotype correlation. METHODS: Keratoplasty tissue from each patient was examined by light and electron microscopy (LM and EM). DNA was obtained, and exons 4 and 12 of BIGH3 were analyzed by polymerase chain reaction and single-stranded conformation polymorphism/heteroduplex analysis. Abnormally migrating products were analyzed by direct sequencing. RESULTS: In two families with type I CDB (CDBI), the R124L mutation was defined. There were light and ultrastructural features of superficial granular dystrophy and atypical banding of the "rod-shaped bodies" ultrastructurally. Patients from three families with "honeycomb" dystrophy were found to carry the R555Q mutation and had characteristic features of Bowman's dystrophy type II (CDBII). CONCLUSIONS: There is a strong genotype:phenotype correlation among CBDI (R124L) and CDBII (R555Q). LM and EM findings suggest that epithelial abnormalities may underlie the pathology of both conditions. The findings clarify the confusion over classification of the Bowman's layer dystrophies.

Local privatization, intermunicipal cooperation, transaction costs and political interests: Evidence from Spain

Several empirical studies have analyzed the factors that influence local privatization. Variables related to fiscal stress, cost reduction, political processes and ideological attitudes are the most common explanatory variables used in these studies. In this paper, we add to this literature by examining the influence of transaction costs and political factors on local governments’ choices through new variables. In addition to this, we consider the role of additional aspects, such as intermunicipal cooperation as a potential alternative to privatization in order to exploit scale economies or scope economies. We consider two relevant services: solid waste collection and water distribution. Results from our estimates show that privatization (that is, contracting out to a private firm) is less common for water distribution than for solid waste collection. Higher transaction costs in water distribution are consistent with this finding. Furthermore, we find that municipalities with a conservative ruling party privatize more often regardless of the ideological orientation of the constituency. This shows that those political interests able to influence local elections are more important in determining the form of delivery than is the basic ideological stance of the constituency. Finally, we find that intermunicipal cooperation is an alternative to local privatization.

Characteristics of Langmuir Turbulence in the Ocean Mixed Layer

This study uses large-eddy simulation (LES) to investigate the characteristics of Langmuir turbulence through the turbulent kinetic energy (TKE) budget. Based on an analysis of the TKE budget a velocity scale for Langmuir turbulence is proposed. The velocity scale depends on both the friction velocity and the surface Stokes drift associated with the wave field. The scaling leads to unique profiles of nondimensional dissipation rate and velocity component variances when the Stokes drift of the wave field is sufficiently large compared to the surface friction velocity. The existence of such a scaling shows that Langmuir turbulence can be considered as a turbulence regime in its own right, rather than a modification of shear-driven turbulence. Comparisons are made between the LES results and observations, but the lack of information concerning the wave field means these are mainly restricted to comparing profile shapes. The shapes of the LES profiles are consistent with observed profiles. The dissipation length scale for Langmuir turbulence is found to be similar to the dissipation length scale in the shear-driven boundary layer. Beyond this it is not possible to test the proposed scaling directly using available data. Entrainment at the base of the mixed layer is shown to be significantly enhanced over that due to normal shear turbulence.

On the generation mechanisms of short-scale unbalanced modes in rotating two-layer flows with vertical shear

We report on the results of a laboratory investigation using a rotating two-layer annulus experiment, which exhibits both large-scale vortical modes and short-scale divergent modes. A sophisticated visualization method allows us to observe the flow at very high spatial and temporal resolution. The balanced long-wavelength modes appear only when the Froude number is supercritical (i.e. $F\,{>}\,F_\mathrm{critical}\,{\equiv}\, \upi^2/2$), and are therefore consistent with generation by a baroclinic instability. The unbalanced short-wavelength modes appear locally in every single baroclinically unstable flow, providing perhaps the first direct experimental evidence that all evolving vortical flows will tend to emit freely propagating inertia–gravity waves. The short-wavelength modes also appear in certain baroclinically stable flows. We infer the generation mechanisms of the short-scale waves, both for the baro-clinically unstable case in which they co-exist with a large-scale wave, and for the baroclinically stable case in which they exist alone. The two possible mechanisms considered are spontaneous adjustment of the large-scale flow, and Kelvin–Helmholtz shear instability. Short modes in the baroclinically stable regime are generated only when the Richardson number is subcritical (i.e. $\hbox{\it Ri}\,{<}\,\hbox{\it Ri}_\mathrm{critical}\,{\equiv}\, 1$), and are therefore consistent with generation by a Kelvin–Helmholtz instability. We calculate five indicators of short-wave generation in the baroclinically unstable regime, using data from a quasi-geostrophic numerical model of the annulus. There is excellent agreement between the spatial locations of short-wave emission observed in the laboratory, and regions in which the model Lighthill/Ford inertia–gravity wave source term is large. We infer that the short waves in the baroclinically unstable fluid are freely propagating inertia–gravity waves generated by spontaneous adjustment of the large-scale flow.

Reactive Halogens in the Marine Boundary Layer (RHaMBLe): the tropical North Atlantic experiments

The NERC UK SOLAS-funded Reactive Halogens in the Marine Boundary Layer (RHaMBLe) programme comprised three field experiments. This manuscript presents an overview of the measurements made within the two simultaneous remote experiments conducted in the tropical North Atlantic in May and June 2007. Measurements were made from two mobile and one ground-based platforms. The heavily instrumented cruise D319 on the RRS Discovery from Lisbon, Portugal to São Vicente, Cape Verde and back to Falmouth, UK was used to characterise the spatial distribution of boundary layer components likely to play a role in reactive halogen chemistry. Measurements onboard the ARSF Dornier aircraft were used to allow the observations to be interpreted in the context of their vertical distribution and to confirm the interpretation of atmospheric structure in the vicinity of the Cape Verde islands. Long-term ground-based measurements at the Cape Verde Atmospheric Observatory (CVAO) on São Vicente were supplemented by long-term measurements of reactive halogen species and characterisation of additional trace gas and aerosol species during the intensive experimental period. This paper presents a summary of the measurements made within the RHaMBLe remote experiments and discusses them in their meteorological and chemical context as determined from these three platforms and from additional meteorological analyses. Air always arrived at the CVAO from the North East with a range of air mass origins (European, Atlantic and North American continental). Trace gases were present at stable and fairly low concentrations with the exception of a slight increase in some anthropogenic components in air of North American origin, though NOx mixing ratios during this period remained below 20 pptv. Consistency with these air mass classifications is observed in the time series of soluble gas and aerosol composition measurements, with additional identification of periods of slightly elevated dust concentrations consistent with the trajectories passing over the African continent. The CVAO is shown to be broadly representative of the wider North Atlantic marine boundary layer; measurements of NO, O3 and black carbon from the ship are consistent with a clean Northern Hemisphere marine background. Aerosol composition measurements do not indicate elevated organic material associated with clean marine air. Closer to the African coast, black carbon and NO levels start to increase, indicating greater anthropogenic influence. Lower ozone in this region is possibly associated with the increased levels of measured halocarbons, associated with the nutrient rich waters of the Mauritanian upwelling. Bromide and chloride deficits in coarse mode aerosol at both the CVAO and on D319 and the continuous abundance of inorganic gaseous halogen species at CVAO indicate significant reactive cycling of halogens. Aircraft measurements of O3 and CO show that surface measurements are representative of the entire boundary layer in the vicinity both in diurnal variability and absolute levels. Above the inversion layer similar diurnal behaviour in O3 and CO is observed at lower mixing ratios in the air that had originated from south of Cape Verde, possibly from within the ITCZ. ECMWF calculations on two days indicate very different boundary layer depths and aircraft flights over the ship replicate this, giving confidence in the calculated boundary layer depth.

Sea-breeze modification of the growth of a marine internal boundary layer

A numerical mesoscale model is used to make a high-resolution simulation of the marine boundary layer in the Persian Gulf, during conditions of offshore flow from Saudi Arabia. A marine internal boundary layer (MIBL) and a sea-breeze circulation (SBC) are found to co-exist. The sea breeze develops in the mid-afternoon, at which time its front is displaced several tens of kilometres offshore. Between the coast and the sea-breeze system, the MIBL that occurs is consistent with a picture described in the existing literature. However, the MIBL is perturbed by the SBC, the boundary layer deepening significantly seaward of the sea-breeze front. Our analysis suggests that this strong, localized deepening is not a direct consequence of frontal uplift, but rather that the immediate cause is the retardation of the prevailing, low-level offshore wind by the SBC. The simulated boundary-layer development can be accounted for by using a simple 1D Lagrangian model of growth driven by the surface heat flux. This model is obtained as a straightforward modification of an established MIBL analytic growth model.

Coupling aerosol surface and bulk chemistry with a kinetic double layer model (K2-SUB): oxidation of oleic acid by ozone

We present a kinetic double layer model coupling aerosol surface and bulk chemistry (K2-SUB) based on the PRA framework of gas-particle interactions (Poschl-Rudich-Ammann, 2007). K2-SUB is applied to a popular model system of atmospheric heterogeneous chemistry: the interaction of ozone with oleic acid. We show that our modelling approach allows de-convoluting surface and bulk processes, which has been a controversial topic and remains an important challenge for the understanding and description of atmospheric aerosol transformation. In particular, we demonstrate how a detailed treatment of adsorption and reaction at the surface can be coupled to a description of bulk reaction and transport that is consistent with traditional resistor model formulations. From literature data we have derived a consistent set of kinetic parameters that characterise mass transport and chemical reaction of ozone at the surface and in the bulk of oleic acid droplets. Due to the wide range of rate coefficients reported from different experimental studies, the exact proportions between surface and bulk reaction rates remain uncertain. Nevertheless, the model results suggest an important role of chemical reaction in the bulk and an approximate upper limit of similar to 10(-11) cm(2) s(-1) for the surface reaction rate coefficient. Sensitivity studies show that the surface accommodation coefficient of the gas-phase reactant has a strong non-linear influence on both surface and bulk chemical reactions. We suggest that K2-SUB may be used to design, interpret and analyse future experiments for better discrimination between surface and bulk processes in the oleic acid-ozone system as well as in other heterogeneous reaction systems of atmospheric relevance.

Reactive Halogens in the Marine Boundary Layer (RHaMBLe): the tropical North Atlantic experiments

The NERC UK SOLAS-funded Reactive Halogens in the Marine Boundary Layer (RHaMBLe) programme comprised three field experiments. This manuscript presents an overview of the measurements made within the two simultaneous remote experiments conducted in the tropical North Atlantic in May and June 2007. Measurements were made from two mobile and one ground-based platforms. The heavily instrumented cruise D319 on the RRS Discovery from Lisbon, Portugal to São Vicente, Cape Verde and back to Falmouth, UK was used to characterise the spatial distribution of boundary layer components likely to play a role in reactive halogen chemistry. Measurements onboard the ARSF Dornier aircraft were used to allow the observations to be interpreted in the context of their vertical distribution and to confirm the interpretation of atmospheric structure in the vicinity of the Cape Verde islands. Long-term ground-based measurements at the Cape Verde Atmospheric Observatory (CVAO) on São Vicente were supplemented by long-term measurements of reactive halogen species and characterisation of additional trace gas and aerosol species during the intensive experimental period. This paper presents a summary of the measurements made within the RHaMBLe remote experiments and discusses them in their meteorological and chemical context as determined from these three platforms and from additional meteorological analyses. Air always arrived at the CVAO from the North East with a range of air mass origins (European, Atlantic and North American continental). Trace gases were present at stable and fairly low concentrations with the exception of a slight increase in some anthropogenic components in air of North American origin, though NOx mixing ratios during this period remained below 20 pptv (note the non-IUPAC adoption in this manuscript of pptv and ppbv, equivalent to pmol mol−1 and nmol mol−1 to reflect common practice). Consistency with these air mass classifications is observed in the time series of soluble gas and aerosol composition measurements, with additional identification of periods of slightly elevated dust concentrations consistent with the trajectories passing over the African continent. The CVAO is shown to be broadly representative of the wider North Atlantic marine boundary layer; measurements of NO, O3 and black carbon from the ship are consistent with a clean Northern Hemisphere marine background. Aerosol composition measurements do not indicate elevated organic material associated with clean marine air. Closer to the African coast, black carbon and NO levels start to increase, indicating greater anthropogenic influence. Lower ozone in this region is possibly associated with the increased levels of measured halocarbons, associated with the nutrient rich waters of the Mauritanian upwelling. Bromide and chloride deficits in coarse mode aerosol at both the CVAO and on D319 and the continuous abundance of inorganic gaseous halogen species at CVAO indicate significant reactive cycling of halogens. Aircraft measurements of O3 and CO show that surface measurements are representative of the entire boundary layer in the vicinity both in diurnal variability and absolute levels. Above the inversion layer similar diurnal behaviour in O3 and CO is observed at lower mixing ratios in the air that had originated from south of Cape Verde, possibly from within the ITCZ. ECMWF calculations on two days indicate very different boundary layer depths and aircraft flights over the ship replicate this, giving confidence in the calculated boundary layer depth.

Generation of inertia-gravity waves in the rotating thermal annulus by a localised boundary layer instability

Waves with periods shorter than the inertial period exist in the atmosphere (as inertia-gravity waves) and in the oceans (as Poincaré and internal gravity waves). Such waves owe their origin to various mechanisms, but of particular interest are those arising either from local secondary instabilities or spontaneous emission due to loss of balance. These phenomena have been studied in the laboratory, both in the mechanically-forced and the thermally-forced rotating annulus. Their generation mechanisms, especially in the latter system, have not yet been fully understood, however. Here we examine short period waves in a numerical model of the rotating thermal annulus, and show how the results are consistent with those from earlier laboratory experiments. We then show how these waves are consistent with being inertia-gravity waves generated by a localised instability within the thermal boundary layer, the location of which is determined by regions of strong shear and downwelling at certain points within a large-scale baroclinic wave flow. The resulting instability launches small-scale inertia-gravity waves into the geostrophic interior of the flow. Their behaviour is captured in fully nonlinear numerical simulations in a finite-difference, 3D Boussinesq Navier-Stokes model. Such a mechanism has many similarities with those responsible for launching small- and meso-scale inertia-gravity waves in the atmosphere from fronts and local convection.