Plasma-derived proteins in airway defence, disease and repair of epithelial injury

One significant characteristic of the airway mucosa in vivo, that cannot easily be mimicked in vitro, is its microcirculation, which generates a highly dynamic, biologically active milieu of plasma-derived molecules that may pass to the airway lumen in vivo. New data on the mechanisms of airway mucosal exudation indicate that the protein systems of circulating plasma may contribute significantly to the biology and immunology of the lamina propria, its surface epithelium and the luminal surface, not only in injured airways, but also in airways that are activated but display no sign of oedema, epithelial disruption, or increased absorption capacity. We suggest that present knowledge of the mechanisms of plasma exudation, together with rapidly emerging information (not detailed herein) on receptors, target cells and cellular responses to the plasma-derived molecules, must be considered in any realistic model that investigates "immuno-inflammatory" mechanisms of the airway mucosa.     

Meal patterns in obese and normal weight men: the ''Gustaf'' study

OBJECTIVE: To compare the reported meal patterns between obese and normal weight men. DESIGN: A dietary survey, by means of 12 repeated telephone-administered 24-hour dietary recalls, was conducted in obese and normal weight men. The study period was three months with all seven days of the week included. The contribution of intake types to the reported daily energy intake (EI) was studied as well as the circadian distribution of EI and the reported number of intakes. SUBJECTS: 86 obese men (BMI 37.7 +/- 4.4 kg/m2, mean +/- SD) from the waiting list of the outpatient clinic completed the study altogether with 61 normal weight men (BMI 23.0 +/- 1.9 kg/m2), randomly selected from the Stockholm County Census Bureau. All men were 20-60 years old. RESULTS: Results were analyzed for Group A = all men who completed the study and for Group B = the men who exceeded the CUT-OFF 1 limit for energy intake (reasonably true report as defined by Goldberg). The obvious under-reporters amounted to 73% of the obese and to 28% of the normal weight men. The meal patterns were similar for the obese and the normal weight men. The greatest contributors to EI in both groups were cooked meals, sandwich meals, snacks and breakfast-like meals. The circadian eating pattern was mainly the same in both obese and normal weight men. The reported number of intakes was 5.3 (median) per day in all obese men vs 5.6 in all the controls (P = 0.02), and in Group B 5.3 s 5.9 (P = 0.16) intakes. No specific "obese eating style' could be detected in this study.     

An annotated corpus for the analysis of VP ellipsis

Verb Phrase Ellipsis (VPE) has been studied in great depth in theoretical linguistics, but empirical studies of VPE are rare. We extend the few previous corpus studies with an annotated corpus of VPE in all 25 sections of the Wall Street Journal corpus (WSJ) distributed with the Penn Treebank. We annotated the raw files using a stand-off annotation scheme that codes the auxiliary verb triggering the elided verb phrase, the start and end of the antecedent, the syntactic type of antecedent (VP, TV, NP, PP or AP), and the type of syntactic pattern between the source and target clauses of the VPE and its antecedent. We found 487 instances of VPE (including predicative ellipsis, antecedent-contained deletion, comparative constructions, and pseudo-gapping) plus 67 cases of related phenomena such as do so anaphora. Inter-annotator agreement was high, with a 0.97 average F-score for three annotators for one section of the WSJ. Our annotation is theory neutral, and has better coverage than earlier efforts that relied on automatic methods, e.g. simply searching the parsed version of the Penn Treebank for empty VP’s achieves a high precision (0.95) but low recall (0.58) when compared with our manual annotation. The distribution of VPE source–target patterns deviates highly from the standard examples found in the theoretical linguistics literature on VPE, once more underlining the value of corpus studies. The resulting corpus will be useful for studying VPE phenomena as well as for evaluating natural language processing systems equipped with ellipsis resolution algorithms, and we propose evaluation measures for VPE detection and VPE antecedent selection. The stand-off annotation is freely available for research purposes.     

Two nonlinear optimization methods for black box identification compared

In this paper, two nonlinear optimization methods for the identification of nonlinear systems are compared. Both methods estimate the parameters of e.g. a polynomial nonlinear state-space model by means of a nonlinear least-squares optimization of the same cost function. While the first method does not estimate the states explicitly, the second method estimates both states and parameters adding an extra constraint equation. Both methods are introduced and their similarities and differences are discussed utilizing simulation data. The unconstrained method appears to be faster and more memory efficient, but the constrained method has a significant advantage as well: it is robust for unstable systems of which bounded input-output data can be measured (e.g. a system captured in a stabilizing feedback loop). Both methods have successfully been applied on real-life measurement data.     

Multiway Spectral Clustering with Out-of-Sample Extensions through Weighted Kernel PCA

A new formulation for multiway spectral clustering is proposed. This method corresponds to a weighted kernel principal component analysis (PCA) approach based on primal-dual least-squares support vector machine (LS-SVM) formulations. The formulation allows the extension to out-of-sample points. In this way, the proposed clustering model can be trained, validated, and tested. The clustering information is contained on the eigendecomposition of a modified similarity matrix derived from the data. This eigenvalue problem corresponds to the dual solution of a primal optimization problem formulated in a high-dimensional feature space. A model selection criterion called the Balanced Line Fit (BLF) is also proposed. This criterion is based on the out-of-sample extension and exploits the structure of the eigenvectors and the corresponding projections when the clusters are well formed. The BLF criterion can be used to obtain clustering parameters in a learning framework. Experimental results with difficult toy problems and image segmentation show improved performance in terms of generalization to new samples and computation times.     

A computational study of vortex-airfoil interaction using high-order finite difference methods

Simulations of the interaction between a vortex and a NACA0012 airfoil are performed with a stable, high-order accurate (in space and time), multi-block finite difference solver for the compressible Navier-Stokes equations.We begin by computing a benchmark test case to validate the code. Next, the flow with steady inflow conditions are computed on several different grids. The resolution of the boundary layer as well as the amount of the artificial dissipation is studied to establish the necessary resolution requirements. We propose an accuracy test based on the weak imposition of the boundary conditions that does not require a grid refinement.Finally, we compute the vortex-airfoil interaction and calculate the lift and drag coefficients. It is shown that the viscous terms add the effect of detailed small scale structures to the lift and drag coefficients.     

Implementation of a Modelica compiler using JastAdd attribute grammars

We have implemented a compiler for key parts of Modelica, an object-oriented language supporting equation-based modeling and simulation of complex physical systems. The compiler is extensible, to support experiments with emerging tools for physical models. To achieve extensibility, the implementation is done declaratively in JastAdd, a metacompilation system supporting modern attribute grammar mechanisms such as reference attributes and nonterminal attributes.This paper reports on experiences from this implementation. For name and type analyses, we illustrate how declarative design strategies, originally developed for a Java compiler, could be reused to support Modelica’s advanced features of multiple inheritance and structural subtyping. Furthermore, we present new general design strategies for declarative generation of target ASTs from source ASTs. We illustrate how these strategies are used to resolve a generics-like feature of Modelica called modifications, and to support flattening, a fundamental part of Modelica compilation. To validate that the approach is practical, we have compared the execution speed of our compiler to two existing Modelica compilers.     

Incremental method evolution in global software product management: A retrospective case study

Company growth in a global setting causes challenges in the adaptation and maintenance of an organization’s methods. In this paper, we will analyze incremental method evolution in software product management in a global environment. We validate a method increment approach, based on method engineering principles, by applying it to a retrospective case study conducted at a large ERP vendor. The results show that the method increment types cover all increments that were found in the case study. Also, we identified the following lessons learned for company growth in a global software product management context: method increment drivers, such as the change of business strategy, vary during evolution; a shared infrastructure is critical for rollout; small increments facilitate gradual process improvement; and global involvement is critical. We then claim that method increments enable software companies to accommodate evolutionary adaptations of development process in agreement with the overall company expansion.