Indexing arbitrary-length kk-mers in sequencing reads

We propose a lightweight data structure for indexing and querying collections of NGS reads data in main memory. The data structure supports the interface proposed in the pioneering work by Philippe et al. for counting and locating $k$-mers in sequencing reads. Our solution, PgSA (pseudogenome suffix array), based on finding overlapping reads, is competitive to the existing algorithms in the space use, query times, or both. The main applications of our index include variant calling, error correction and analysis of reads from RNA-seq experiments

Field theory on κ\kappa--Minkowski space revisited: Noether charges and breaking of Lorentz symmetry

This paper is devoted to detailed investigations of free scalar field theory on $\kappa$-Minkowski space. After reviewing necessary mathematical tools we discuss in depth the Lagrangian and solutions of field equations. We analyze the spacetime symmetries of the model and construct the conserved charges associated with translational and Lorentz symmetry. We show that the version of the theory usually studied breaks Lorentz invariance in a subtle way: There is an additional trans-Planckian mode present, and an associated conserved charge (the number of such modes) is not a Lorentz scalar.Comment: 22 pages, 1 figure, formulas in sect. III correcte

Doubly Special Relativity and de Sitter space

In this paper we recall the construction of Doubly Special Relativity (DSR) as a theory with energy-momentum space being the four dimensional de Sitter space. Then the bases of the DSR theory can be understood as different coordinate systems on this space. We investigate the emerging geometrical picture of Doubly Special Relativity by presenting the basis independent features of DSR that include the non-commutative structure of space-time and the phase space algebra. Next we investigate the relation between our geometric formulation and the one based on quantum $\kappa$-deformations of the Poincar\'e algebra. Finally we re-derive the five-dimensional differential calculus using the geometric method, and use it to write down the deformed Klein-Gordon equation and to analyze its plane wave solutions.Comment: 26 pages, one formula (67) corrected; some remarks adde

Long bone metastases as predictors of survival in patients with metastatic renal cancer

BACKGROUND: The aim of this study was to assess the prevalence of long bone metastases in renal cancer patients and to evaluate their utility as predictors of survival in this group. MATERIAL AND METHODS: This retrospective study included 20 patients with metastatic renal cancer and bone metastases. The patients were referred for regular bone scintigraphy in order to assess disease spread in the skeleton. The patients were divided into two groups: those with 1) metastases in the skeleton (including long bones) and those with 2) metastases in the axial skeleton only. RESULTS: Bone scintigraphy imaging was performed regularly up to 81 months from the first positive bone scan. During that time 11 deaths (8 among patients with long bone lesions) were recorded. Kaplan-Meyer curves showed that patients with long bone metastases tend to have lower survival probability in comparison to the ones with metastases in other bones. CONCLUSIONS: Bone metastases localization seems to influence survival in patients with renal cancer. Long bone-involving spread of the disease is associated with worse survival probability than the spread to the other bones

Proper Layering Is Important for Precisely Timed Activation of Hippocampal Mossy Cells

The mammalian cortex exhibits a laminated structure that may underlie optimal synaptic connectivity and support temporally precise activation of neurons. In ‘reeler' mice, the lack of the extracellular matrix protein Reelin leads to abnormal positioning of cortical neurons and disrupted layering. To address how these structural changes impact neuronal function, we combined electrophysiological and neuroanatomical techniques to investigate the synaptic activation of hippocampal mossy cells (MCs), the cell type that integrates the output of dentate gyrus granule cells (GCs). While somatodendritic domains of wild-type (WT) MCs were confined to the hilus, the somata and dendrites of reeler MCs were often found in the molecular layer, where the perforant path (PP) terminates. Most reeler MCs received aberrant monosynaptic excitatory input from the PP, whereas the disynaptic input to MCs via GCs was decreased and inhibition was increased. In contrast to the uniform disynaptic discharge of WT MCs, many reeler cells discharged with short, monosynaptic latencies, while others fired with long latencies over a broad temporal window in response to PP activation. Thus, disturbed lamination results in aberrant synaptic connectivity and altered timing of action potential generation. These results highlight the importance of a layered cortical structure for information processin