MINRbase: a comprehensive database of nuclear- and mitochondrial-ribosomal-RNA-derived fragments (rRFs).

We describe the Mitochondrial and Nuclear rRNA fragment database (MINRbase), a knowledge repository aimed at facilitating the study of ribosomal RNA-derived fragments (rRFs). MINRbase provides interactive access to the profiles of 130 238 expressed rRFs arising from the four human nuclear rRNAs (18S, 5.8S, 28S, 5S), two mitochondrial rRNAs (12S, 16S) or four spacers of 45S pre-rRNA. We compiled these profiles by analyzing 11 632 datasets, including the GEUVADIS and The Cancer Genome Atlas (TCGA) repositories. MINRbase offers a user-friendly interface that lets researchers issue complex queries based on one or more criteria, such as parental rRNA identity, nucleotide sequence, rRF minimum abundance and metadata keywords (e.g. tissue type, disease). A 'summary' page for each rRF provides a granular breakdown of its expression by tissue type, disease, sex, ancestry and other variables; it also allows users to create publication-ready plots at the click of a button. MINRbase has already allowed us to generate support for three novel observations: the internal spacers of 45S are prolific producers of abundant rRFs; many abundant rRFs straddle the known boundaries of rRNAs; rRF production is regimented and depends on 'personal attributes' (sex, ancestry) and 'context' (tissue type, tissue state, disease). MINRbase is available at https://cm.jefferson.edu/MINRbase/.

The subcellular distribution of miRNA isoforms, tRNA-derived fragments, and rRNA-derived fragments depends on nucleotide sequence and cell type.

BACKGROUND: MicroRNA isoforms (isomiRs), tRNA-derived fragments (tRFs), and rRNA-derived fragments (rRFs) represent most of the small non-coding RNAs (sncRNAs) found in cells. Members of these three classes modulate messenger RNA (mRNA) and protein abundance and are dysregulated in diseases. Experimental studies to date have assumed that the subcellular distribution of these molecules is well-understood, independent of cell type, and the same for all isoforms of a sncRNA. RESULTS: We tested these assumptions by investigating the subcellular distribution of isomiRs, tRFs, and rRFs in biological replicates from three cell lines from the same tissue and same-sex donors that model the same cancer subtype. In each cell line, we profiled the isomiRs, tRFs, and rRFs in the nucleus, cytoplasm, whole mitochondrion (MT), mitoplast (MP), and whole cell. Using a rigorous mathematical model we developed, we accounted for cross-fraction contamination and technical errors and adjusted the measured abundances accordingly. Analyses of the adjusted abundances show that isomiRs, tRFs, and rRFs exhibit complex patterns of subcellular distributions. These patterns depend on each sncRNA's exact sequence and the cell type. Even in the same cell line, isoforms of the same sncRNA whose sequences differ by a few nucleotides (nts) can have different subcellular distributions. CONCLUSIONS: SncRNAs with similar sequences have different subcellular distributions within and across cell lines, suggesting that each isoform could have a different function. Future computational and experimental studies of isomiRs, tRFs, and rRFs will need to distinguish among each molecule's various isoforms and account for differences in each isoform's subcellular distribution in the cell line at hand. While the findings add to a growing body of evidence that isomiRs, tRFs, rRFs, tRNAs, and rRNAs follow complex intracellular trafficking rules, further investigation is needed to exclude alternative explanations for the observed subcellular distribution of sncRNAs.

Robot Navigation in Complex Workspaces Employing Harmonic Maps and Adaptive Artificial Potential Fields.

In this work, we address the single robot navigation problem within a planar and arbitrarily connected workspace. In particular, we present an algorithm that transforms any static, compact, planar workspace of arbitrary connectedness and shape to a disk, where the navigation problem can be easily solved. Our solution benefits from the fact that it only requires a fine representation of the workspace boundary (i.e., a set of points), which is easily obtained in practice via SLAM. The proposed transformation, combined with a workspace decomposition strategy that reduces the computational complexity, has been exhaustively tested and has shown excellent performance in complex workspaces. A motion control scheme is also provided for the class of non-holonomic robots with unicycle kinematics, which are commonly used in most industrial applications. Moreover, the tuning of the underlying control parameters is rather straightforward as it affects only the shape of the resulted trajectories and not the critical specifications of collision avoidance and convergence to the goal position. Finally, we validate the efficacy of the proposed navigation strategy via extensive simulations and experimental studies.

Navigation of Multiple Disk-Shaped Robots with Independent Goals within Obstacle-Cluttered Environments.

In this work, we propose a hybrid control scheme to address the navigation problem for a team of disk-shaped robotic platforms operating within an obstacle-cluttered planar workspace. Given an initial and a desired configuration of the system, we devise a hierarchical cell decomposition methodology which is able to determine which regions of the configuration space need to be further subdivided at each iteration, thus avoiding redundant cell expansions. Furthermore, given a sequence of free configuration space cells with an arbitrary connectedness and shape, we employ harmonic transformations and harmonic potential fields to accomplish safe transitions between adjacent cells, thus ensuring almost-global convergence to the desired configuration. Finally, we present the comparative simulation results that demonstrate the efficacy of the proposed control scheme and its superiority in terms of complexity while yielding a satisfactory performance without incorporating optimization in the selection of the paths.