Mining, compressing and classifying with extensible motifs

BACKGROUND: Motif patterns of maximal saturation emerged originally in contexts of pattern discovery in biomolecular sequences and have recently proven a valuable notion also in the design of data compression schemes. Informally, a motif is a string of intermittently solid and wild characters that recurs more or less frequently in an input sequence or family of sequences. Motif discovery techniques and tools tend to be computationally imposing, however, special classes of "rigid" motifs have been identified of which the discovery is affordable in low polynomial time. RESULTS: In the present work, "extensible" motifs are considered such that each sequence of gaps comes endowed with some elasticity, whereby the same pattern may be stretched to fit segments of the source that match all the solid characters but are otherwise of different lengths. A few applications of this notion are then described. In applications of data compression by textual substitution, extensible motifs are seen to bring savings on the size of the codebook, and hence to improve compression. In germane contexts, in which compressibility is used in its dual role as a basis for structural inference and classification, extensible motifs are seen to support unsupervised classification and phylogeny reconstruction. CONCLUSION: Off-line compression based on extensible motifs can be used advantageously to compress and classify biological sequences

SEM2: Introducing mechanics in cell and tissue modeling using coarse-grained homogeneous particle dynamics

Modeling multiscale mechanics in shape-shifting engineered tissues, such as organoids and organs-on-chip, is both important and challenging. In fact, it is difficult to model relevant tissue-level large non-linear deformations mediated by discrete cell-level behaviors, such as migration and proliferation. One approach to solve this problem is subcellular element modeling (SEM), where ensembles of coarse-grained particles interacting via empirically defined potentials are used to model individual cells while preserving cell rheology. However, an explicit treatment of multiscale mechanics in SEM was missing. Here, we incorporated analyses and visualizations of particle level stress and strain in the open-source software SEM++ to create a new framework that we call subcellular element modeling and mechanics or SEM2. To demonstrate SEM2, we provide a detailed mechanics treatment of classical SEM simulations including single-cell creep, migration, and proliferation. We also introduce an additional force to control nuclear positioning during migration and proliferation. Finally, we show how SEM2 can be used to model proliferation in engineered cell culture platforms such as organoids and organs-on-chip. For every scenario, we present the analysis of cell emergent behaviors as offered by SEM++ and examples of stress or strain distributions that are possible with SEM2. Throughout the study, we only used first-principles literature values or parametric studies, so we left to the Discussion a qualitative comparison of our insights with recently published results. The code for SEM2 is available on GitHub at https://github.com/Synthetic-Physiology-Lab/sem2

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Not AvailableLand resource is finite and competing demands for land are infinite. Arable land is shrinking because of diversion of agricultural lands to other non-agricultural uses and agriculture related activities are being taken up on marginal lands. This has resulted in land degradation and land resource management is considered as one of the priority areas for achieving sustainable food security by raising land productivity. The concept of using the land for suitable utilization lies within the land use planning (LUP) process, which aims at optimizing the use of land while sustaining its potential by avoiding resource degradation. It has been recognized that the land assessment and its reliability for land use decisions depend largely on the quality of soil information. Efforts were made to develop regional level land use plans by using land resource information generated at small scale (1:250,000 and 1:50,000). However, the efforts could not yield desired results at village level due to unavailability of large scale land resources database. Stakeholders seldom adopted these land use plans due to lack of site-specific information. Land Resource Inventory (LRI) at large scale (1:10,000) provides required information to prepare sustainable land use plan at village level, which sets the path for using right land use and right agro-techniques on each parcel of land. In India, LUP at local level are governed by farmers own requirement and market prices rather than land suitability criteria alone. LUP aims to encourage and assist land users in selecting options that increase their productivity, are sustainable and meet the needs of society. The systematic evaluation and planning of land resources requires basic data and information about the land, the people and the organization of administration and service. Participatory land use planning (PLUP) approach helps greatly in developing site-specific land resource management options to improve the land productivity and to minimize land degradation.Not Availabl