Partial chord diagrams and matrix models

In this article, the enumeration of partial chord diagrams is discussed via matrix model techniques. In addition to the basic data such as the number of backbones and chords, we also consider the Euler characteristic, the backbone spectrum, the boundary point spectrum, and the boundary length spectrum. Furthermore, we consider the boundary length and point spectrum that unifies the last two types of spectra. We introduce matrix models that encode generating functions of partial chord diagrams filtered by each of these spectra. Using these matrix models, we derive partial differential equations - obtained independently by cut-and-join arguments in an earlier work - for the corresponding generating functions.Comment: 42 pages, 14 figure

BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction

A novel discrete mathematical approach is proposed as an additional tool for molecular systematics which does not require prior statistical assumptions concerning the evolutionary process. The method is based on algorithms generating mathematical representations directly from DNA/RNA or protein sequences, followed by the output of numerical (scalar or vector) and visual characteristics (graphs). The binary encoded sequence information is transformed into a compact analytical form, called the Iterative Canonical Form (or ICF) of Boolean functions, which can then be used as a generalized molecular descriptor. The method provides raw vector data for calculating different distance matrices, which in turn can be analyzed by neighbor-joining or UPGMA to derive a phylogenetic tree, or by principal coordinates analysis to get an ordination scattergram. The new method and the associated software for inferring phylogenetic trees are called the Boolean analysis or BOOL-AN

Aerospace medicine and biology: A continuing bibliography with indexes (supplement 333)

This bibliography lists 122 reports, articles and other documents introduced into the NASA Scientific and Technical Information System during January, 1990. Subject coverage includes: aerospace medicine and psychology, life support systems and controlled environments, safety equipment, exobiology and extraterrestrial life, and flight crew behavior and performance

Fully-Functional Bidirectional Burrows-Wheeler Indexes and Infinite-Order De Bruijn Graphs

Given a string T on an alphabet of size sigma, we describe a bidirectional Burrows-Wheeler index that takes O(|T| log sigma) bits of space, and that supports the addition and removal of one character, on the left or right side of any substring of T, in constant time. Previously known data structures that used the same space allowed constant-time addition to any substring of T, but they could support removal only from specific substrings of T. We also describe an index that supports bidirectional addition and removal in O(log log |T|) time, and that takes a number of words proportional to the number of left and right extensions of the maximal repeats of T. We use such fully-functional indexes to implement bidirectional, frequency-aware, variable-order de Bruijn graphs with no upper bound on their order, and supporting natural criteria for increasing and decreasing the order during traversal

ROCK signaling promotes collagen remodeling to facilitate invasive pancreatic ductal adenocarcinoma tumor cell growth

Pancreatic ductal adenocarcinoma (PDAC) is a major cause of cancer death; identifying PDAC enablers may reveal potential therapeutic targets. Expression of the actomyosin regulatory ROCK1 and ROCK2 kinases increased with tumor progression in human and mouse pancreatic tumors, while elevated ROCK1/ROCK2 expression in human patients, or conditional ROCK2 activation in a KrasG12D/p53R172H mouse PDAC model, was associated with reduced survival. Conditional ROCK1 or ROCK2 activation promoted invasive growth of mouse PDAC cells into three‐dimensional collagen matrices by increasing matrix remodeling activities. RNA sequencing revealed a coordinated program of ROCK‐induced genes that facilitate extracellular matrix remodeling, with greatest fold‐changes for matrix metalloproteinases (MMPs) Mmp10 and Mmp13. MMP inhibition not only decreased collagen degradation and invasion, but also reduced proliferation in three‐dimensional contexts. Treatment of KrasG12D/p53R172H PDAC mice with a ROCK inhibitor prolonged survival, which was associated with increased tumor‐associated collagen. These findings reveal an ancillary role for increased ROCK signaling in pancreatic cancer progression to promote extracellular matrix remodeling that facilitates proliferation and invasive tumor growth

Rigidity and flexibility of biological networks

The network approach became a widely used tool to understand the behaviour of complex systems in the last decade. We start from a short description of structural rigidity theory. A detailed account on the combinatorial rigidity analysis of protein structures, as well as local flexibility measures of proteins and their applications in explaining allostery and thermostability is given. We also briefly discuss the network aspects of cytoskeletal tensegrity. Finally, we show the importance of the balance between functional flexibility and rigidity in protein-protein interaction, metabolic, gene regulatory and neuronal networks. Our summary raises the possibility that the concepts of flexibility and rigidity can be generalized to all networks.Comment: 21 pages, 4 figures, 1 tabl