Text in Diagrams: Challenges to and Opportunities of Automatic Layout

Visual programming languages based on node-link diagrams are supposedly easy to use and to understand. This is only true, however, if the diagram elements are properly placed - a tedious and time-consuming process if done manually. Automatic graph layout algorithms alleviate users from that burden. Since even visual languages usually cannot make do without text, it follows that layout algorithms need to properly support textual labels. That is what this work is all about. We start by examining how enough space can be reserved for textual labels to be properly placed without overlaps. We then look at how users place comments in diagrams to establish relations to diagram elements. Our aim is to infer those, in order to take them into account during layout. We finally look at the negative implications of too much text: large diagrams and too much information. Different label management strategies dynamically change the text of labels, thus changing their size and, optionally, the amount of text displayed. All of the techniques are evaluated according to aesthetic criteria, and most are also validated through user studies

Using One-Dimensional Compaction for Smaller Graph Drawings

We review the technique of one-dimensional compaction and use it as part of two new methods tackling problems in the context of automatic diagram layout: First, a postprocessing of the layer-based layout algorithm, also known as Sugiyama layout, and second a placement algorithm for connected components with external extensions. We apply our methods to dataflow diagrams from practical applications and find that the first method significantly reduces the width of left-to-right drawn diagrams. The second method allows to properly arrange disconnected graphs that have hierarchycrossing edges. Keywords: one-dimensional compaction, diagram layout, layer-based layout, Sugiyama layout, disconnected graphs, dataflow diagram

Automatic Layout and Label Management for UML Sequence Diagrams

Sequence diagrams belong to the most commonly used types of UML diagrams. There is research on desirable aesthetics, but to our knowledge no published layout algorithms, although several have been developed. This might be due to the rigid specifcation of sequence diagrams that seems to make laying them out quite easy. However, as we argue here, naive algorithms do not always produce desirable solutions. We present a layout algorithm that can compute the order of lifelines according to different optimization criteria. We also look at the problem of diagram size by introducing vertical compaction to sequence diagrams and by applying label management to compact them horizontally. We evaluate our methods with 50 real-world sequence diagrams

On Comments in Visual Languages

Visual languages based on node-link diagrams can be used to develop software and, like textual languages, offer the possibility to write explanatory comments. Which node a comment refers to is usually not made explicit, but is implicitly clear to readers through placement and content. While automatic layout algorithms can make working with diagrams more productive, they tend to destroy such implicit clues because they are not aware of them and thus do not preserve the relative placement of comments and the nodes they refer to. Implicit clues thus need to be inferred and made explicit to be taken into account by layout algorithms. This is what we call the comment attachment problem. In this paper, we improve upon a previous paper on the subject [9], introducing further heuristics that aim to describe relations between comments and nodes. Based on an analysis of comment placement in a set of example diagrams, we develop a general comment attachment framework and evaluate the quality of its inferred attachments

Drawing Layered Hypergraphs

Orthogonally drawn hypergraphs have important applications, e.g. in actor-oriented data flow diagrams for modeling complex software systems. Graph drawing algorithms based on the approach by Sugiyama et al. place nodes into consecutive layers and try to minimize the number of edge crossings by finding suitable orderings of the nodes in each layer. With orthogonal hyperedges, however, the exact number of crossings is not determined until the edges are actually routed in a later phase of the algorithm, which makes it hard to evaluate the quality of a given node ordering beforehand. In this report, we present and evaluate two crossing counting algorithms that predict the number of crossings between orthogonally routed hyperedges much more accurately than previous methods. We also describe methods for routing hyperedges that span multiple layers and for handling junction points

Comparative Study of the Tempering Behavior of Different Martensitic Steels by Means of In-Situ Diffractometry and Dilatometry

Martensitic steels are tempered to increase the toughness of the metastable martensite, which is brittle in the as-quenched state, and to achieve a more stable microstructure. During the tempering of steels, several particular overlapping effects can arise. Classical dilatometric investigations can only detect effects by monitoring the integral length change of the sample. Additional in-situ diffractometry allowed a differentiation of the individual effects such as transformation of retained austenite and formation of cementite during tempering. Additionally, the lattice parameters of martensite and therefrom the tetragonality was analyzed. Two low-alloy steels with carbon contents of 0.4 and 1.0 wt.% and a high-alloy 5Cr-1Mo-steel with 0.4 wt.% carbon were investigated by dilatometry and in-situ diffractometry. In this paper, microstructural effects during tempering of the investigated steels are discussed by a comparative study of dilatometric and diffractometric experiments. The influence of the chemical composition on the tempering behavior is illustrated by comparing the determined effects of the three steels. The kinetics of tempering is similar for the low-alloy steels and shifted to much higher temperatures for the high-alloy steel. During tempering, the tetragonality of martensite in the steel with 1.0 wt% carbon shifts towards a low carbon behavior, as in the steels with 0.4 wt.% carbon

MyD88 Is Required for Efficient Control of Coxiella burnetii Infection and Dissemination

The intracellular pathogen Coxiella (C.) burnetii causes Q fever, a usually self-limiting respiratory infection that becomes chronic and severe in some patients. Innate immune recognition of C. burnetii and its role in the decision between resolution and chronicity is not understood well. However, TLR2 is important for the response to C. burnetii in mice, and genetic polymorphisms in Myd88 have been associated with chronic Q fever in humans. Here, we have employed MyD88-deficient mice in infection models with the attenuated C. burnetii Nine Mile phase II strain (NMII). Myd88−/− macrophages failed to restrict the growth of NMII in vitro, and to upregulate production of the cytokines TNF, IL-6, and IL-10. Following intraperitoneal infection, NMII bacterial burden was significantly higher on day 5 and 20 in organs of Myd88−/− mice. After infection via the natural route by intratracheal injection, a higher bacterial load in the lung and increased dissemination of NMII to other organs was observed in MyD88-deficient mice. While wild-type mice essentially cleared NMII on day 27 after intratracheal infection, it was still readily detectable on day 42 in multiple organs in the absence of MyD88. Despite the elevated bacterial load, Myd88−/− mice had less granulomatous inflammation and expressed significantly lower levels of chemoattractants, inflammatory cytokines, and of several IFNγ-induced genes relevant for control of intracellular pathogens. Together, our results show that MyD88-dependent signaling is essential for early control of C. burnetii replication and to prevent systemic spreading. The continued presence of NMII in the organs of Myd88−/− mice constitutes a new mouse model to study determinants of chronicity and resolution in Q fever

Caloric restriction and intermittent fasting alter hepatic lipid droplet proteome and diacylglycerol species and prevent diabetes in NZO mice

AbstractCaloric restriction and intermittent fasting are known to improve glucose homeostasis and insulin resistance in several species including humans. The aim of this study was to unravel potential mechanisms by which these interventions improve insulin sensitivity and protect from type 2 diabetes. Diabetes-susceptible New Zealand Obese mice were either 10% calorie restricted (CR) or fasted every other day (IF), and compared to ad libitum (AL) fed control mice. AL mice showed a diabetes prevalence of 43%, whereas mice under CR and IF were completely protected against hyperglycemia. Proteomic analysis of hepatic lipid droplets revealed significantly higher levels of PSMD9 (co-activator Bridge-1), MIF (macrophage migration inhibitor factor), TCEB2 (transcription elongation factor B (SIII), polypeptide 2), ACY1 (aminoacylase 1) and FABP5 (fatty acid binding protein 5), and a marked reduction of GSTA3 (glutathione S-transferase alpha 3) in samples of CR and IF mice. In addition, accumulation of diacylglycerols (DAGs) was significantly reduced in livers of IF mice (P=0.045) while CR mice showed a similar tendency (P=0.062). In particular, 9 DAG species were significantly reduced in response to IF, of which DAG-40:4 and DAG-40:7 also showed significant effects after CR. This was associated with a decreased PKCε activation and might explain the improved insulin sensitivity. In conclusion, our data indicate that protection against diabetes upon caloric restriction and intermittent fasting associates with a modulation of lipid droplet protein composition and reduction of intracellular DAG species

Expression of S-locus inhibitor gene (Sli) in various diploid potatoes

Current guidelines recommend immunosuppressive treatment (IT) in patients with primary sclerosing cholangitis (PSC) and elevated aminotransferase levels more than five times the upper limit of normal and elevated serum IgG-levels above twice the upper limit of normal. Since there is no evidence to support this recommendation, we aimed to assess the criteria that guided clinicians in clinical practice to initiate IT in patients with previously diagnosed PSC.This is a retrospective analysis of 196 PSC patients from seven German hepatology centers, of whom 36 patients had received IT solely for their liver disease during the course of PSC. Analyses were carried out using methods for competing risks.A simplified autoimmune hepatitis (AIH) score >5 (HR of 36, p5 and a mHAI score >3, suggesting concomitant features of AIH, influenced the decision to introduce IT during the course of PSC. In German clinical practice, the cutoffs used to guide IT may be lower than recommended by current guidelines