Hypergraph Grammars in hp-adaptive Finite Element Method

AbstractThe paper presents the hypergraph grammar for modelling the hp-adaptive finite element method algorithm with rectangular elements. The finite element mesh is represented by a hypergraph. All mesh transformations are modelled by means of hypergraph grammar rules. These rules allow to generate the initial mesh, to assign values of polynomial order to the element nodes, to generate the matrix for each element, to solve the problem and to perform the hp-adaptation

Quantifying coincidence in non-uniform time series with mutual graph approximation : speech and ECG examples

Compressive sensing and arbitrary sampling are techniques of data volume reduction challenging the Shannon sampling theorem and expected to provide efficient storage while preserving original information. Irregularity of sampling is either a result of intentional optimization of a sampling grid or stems from sporadic occurrence or intermittent observability of a phenomenon. Quantitative comparison of irregular patterns similarity is usually preceded by a projection to a regular sampling space. In this paper, we study methods for direct comparison of time series in their original non-uniform grids. We also propose a linear graph to be a representation of the non-uniform signal and apply the Mutual Graph Approximation (MGA) method as a metric to infer the degree of similarity of the considered patterns. The MGA was implemented together with four state-of-the-art methods and tested with example speech signals and electrocardiograms projected to bandwidth-related and random sampling grids. Our results show that the performance of the proposed MGA method is comparable to most accurate (correlation of 0.964 vs. Frechet: 0.962 and Kleinberg: 0.934 for speech signals) and to less computationally expensive state-of-the-art distance metrics (both MGA and Hausdorf: O(L$_{1}$ + L$_{2}$)). Moreover, direct comparison of non-uniform signals can be equivalent to cross-correlation of resampled signals (correlation of 0.964 vs. resampled: 0.960 for speech signals, and 0.956 vs. 0.966 for electrocardiograms) in applications as signal classification in both accuracy and computational complexity. Finally, the bandwidth-based resampling model plays a substantial role; usage of random grid is the primary cause of inaccuracy (correlation of 0.960 vs. for random sampling grid: 0.900 for speech signals, and 0.966 vs. 0.878, respectively, for electrocardiograms). These figures indicate that the proposed MGA method can be used as a simple yet effective tool for scoring similarity of signals directly in non-uniform sampling grids

A multi-agent system in education facility design

This paper deals with a multi-agent system which supports the designer in solving complex design tasks. The behaviour of design agents is modelled by sets of grammar rules. Each agent uses a graph grammar or a shape grammar and a database of facts concerning the subtask it is responsible for. The course of the design process is determined by the interaction between specialised agents. Space layouts of designs are represented by attributed graphs encoding both topological structures and semantic properties of solutions. The agents work in parallel on the common graph, independently generating layouts of different design components while specified node labels evoke agents using shape grammars. The agents’ cooperation allows them to combine a form-oriented approach with a functional-structural one in the design process, where the agents generate the general 3D form of the object based on design requirements together with the space layout based on the functional aspects of the solution. Based on the given design criteria, the agents search for admissible solutions within the design space that constitutes their operating environment. The proposed approach is illustrated by the example of designing kindergarten facilities

Parameterized IFC-based graph generation for user-oriented path search

This paper deals with the problem of transforming the data obtained from the IFC file of a given building into a weighted graph, which is used for searching shortest routes accessible for different types of users including people and mobile objects. This graph contains information about the topology and accessibility between building spaces. It is created using the parameter specifying the permissible distance from the center of a moving object to a wall. Edge weights are calculated based on the Euclidean distance between nodes representing doors or internal points of rooms with concave shapes. On the basis of information encoded in the graph the application calculates the shortest path between designated rooms and creates its visualization. The presented approach is illustrated on examples of searching shortest routs between spaces of the building extracted from the IFC file belonging to the free IFC model database

Visual Design and Reasoning with the Use of Hypergraph Transformations

This paper deals with visual design and reasoning. A visual language with its internal representation in the form of attributed hierarchical hypergraphs is discussed. Hypergraph attributes allow for defining and analysing constraints imposed by design knowledge. Operations on hypergraphs which reflect modifications of design diagrams are also presented. The approach is illustrated by examples of designing floor-layouts

Macrofungi of the Bieszczady Mountains

The Bieszczady Mts, a mountain range in SE Poland, is a hot spot of fungal richness and diversity in Poland. This paper summarizes 5 years of studies in the Bieszczady Mts, as well as previously published research. A total of 1,377 macromycetes taxa were found, including many (464) which were protected, red-listed, or very rare in Poland. Thirty-eight taxa (nine Ascomycota and 29 Basidiomycota) have been reported in Poland for the first time: Agrocybe gibberosa, Auriporia aurulenta, Bolbitius variicolor, Bulgariella pulla, Chaetosphaerella phaeostroma, Clitocybe subspadicea, Clitopilus passeckerianus, Cortinarius anomalus var. subcaligatus, C. fervidus, C. flexipes var. inolens, C. sylvae-norvegicae, Cudoniella tenuispora, Entoloma bisporigerum, E. olorinum, E. poliopus var. parvisporigerum, E. sericeoides, Galerina caulocystidiata, Gymnopilus josserandii, Hymenoscyphus subferrugineus, Hypholoma olivaceotinctum, Inocybe queletii, Laccaria altaica, Lactarius romagnesii, L. rostratus, Mycena epipterygia var. atroviscosa, M. epipterygia var. candida, M. polygramma f. candida, Octavianina lutea, O. mutabilis, Pachyella violaceonigra, Panaeolus papilionaceus var. capitatocystis, Phaeocollybia jennyae, Psathyrella almerensis, Pyrenopeziza inornata, Scutellinia torrentis, Tricholoma basirubens, Tricholomopsis flammula, and Vibrissea decolorans. For all new taxa, short descriptions based on the collected material have been provided

Changepoint Detection in Noisy Data Using a Novel Residuals Permutation-Based Method (RESPERM): Benchmarking and Application to Single Trial ERPs

An important problem in many fields dealing with noisy time series, such as psychophysiological single trial data during learning or monitoring treatment effects over time, is detecting a change in the model underlying a time series. Here, we present a new method for detecting a single changepoint in a linear time series regression model, termed residuals permutation-based method (RESPERM). The optimal changepoint in RESPERM maximizes Cohen’s effect size with the parameters estimated by the permutation of residuals in a linear model. RESPERM was compared with the SEGMENTED method, a well-established and recommended method for detecting changepoints, using extensive simulated data sets, varying the amount and distribution characteristics of noise and the location of the change point. In time series with medium to large amounts of noise, the variance of the detected changepoint was consistently smaller for RESPERM than SEGMENTED. Finally, both methods were applied to a sample dataset of single trial amplitudes of the N250 ERP component during face learning. In conclusion, RESPERM appears to be well suited for changepoint detection especially in noisy data, making it the method of choice in neuroscience, medicine and many other fields.Peer Reviewe

A novel, pan-PDE inhibitor exerts anti-fibrotic effects in human lung fibroblasts via inhibition of TGF-β\beta signaling and activation of cAMP/PKA signaling

Phosphodiesterase (PDE) inhibitors are currently a widespread and extensively studied group of anti-inflammatory and anti-fibrotic compounds which may find use in the treatment of numerous lung diseases, including asthma and chronic obstructive pulmonary disease. Several PDE inhibitors are currently in clinical development, and some of them, e.g., roflumilast, are already recommended for clinical use. Due to numerous reports indicating that elevated intracellular cAMP levels may contribute to the alleviation of inflammation and airway fibrosis, new and effective PDE inhibitors are constantly being sought. Recently, a group of 7,8-disubstituted purine-2,6-dione derivatives, representing a novel and prominent pan-PDE inhibitors has been synthesized. Some of them were reported to modulate transient receptor potential ankyrin 1 (TRPA1) ion channels as well. In this study, we investigated the effect of selected derivatives (832-a pan-PDE inhibitor, 869-a TRPA1 modulator, and 145-a pan-PDE inhibitor and a weak TRPA1 modulator) on cellular responses related to airway remodeling using MRC-5 human lung fibroblasts. Compound 145 exerted the most considerable effect in limiting fibroblast to myofibroblasts transition (FMT) as well as proliferation, migration, and contraction. The effect of this compound appeared to depend mainly on its strong PDE inhibitory properties, and not on its effects on TRPA1 modulation. The strong anti-remodeling effects of 145 required activation of the cAMP/protein kinase A (PKA)/cAMP response element-binding protein (CREB) pathway leading to inhibition of transforming growth factor type β1 (TGF-β1) and Smad-dependent signaling in MRC-5 cells. These data suggest that the TGF-β pathway is a major target for PDE inhibitors leading to inhibitory effects on cell responses involved in airway remodeling. These potent, pan-PDE inhibitors from the group of 7,8-disubstituted purine-2,6-dione derivatives, thus represent promising anti-remodeling drug candidates for further research