Comparison of algorithms for identification of IIR systems from binary measurements on the output

In the last decade, a significant number of algorithms of systems using only a quantized output, has appeared. In this study, an overview of identification methods of IIR systems, using quantized or binary output, is presented. A short description of the methods existing in the literature is given. The methods are compared both on the basis of simulation examples.

GenMap: ultra-fast computation of genome mappability

Motivation Computing the uniqueness of k-mers for each position of a genome while allowing for up to e mismatches is computationally challenging. However, it is crucial for many biological applications such as the design of guide RNA for CRISPR experiments. More formally, the uniqueness or (k, e)-mappability can be described for every position as the reciprocal value of how often this k-mer occurs approximately in the genome, i.e. with up to e mismatches. Results We present a fast method GenMap to compute the (k, e)-mappability. We extend the mappability algorithm, such that it can also be computed across multiple genomes where a k-mer occurrence is only counted once per genome. This allows for the computation of marker sequences or finding candidates for probe design by identifying approximate k-mers that are unique to a genome or that are present in all genomes. GenMap supports different formats such as binary output, wig and bed files as well as csv files to export the location of all approximate k-mers for each genomic position. Availability and implementation GenMap can be installed via bioconda. Binaries and C++ source code are available on https://github.com/cpockrandt/genmap.

Notch pathway: a bistable inducer of biological noise?

Notch signalling pathway is central to development of metazoans. The pathway codes a binary fate switch. Upon activation, downstream signals contribute to resolution of fate dichotomies such as proliferation/differentiation or sub-lineage differentiation outcome. There is, however, an interesting paradox in the Notch signalling pathway. Despite remarkable predictability of fate outcomes instructed by the Notch pathway, the associated transcriptome is versatile and plastic. This inconsistency suggests the presence of an interface that compiles input from the plastic transcriptome of the Notch pathway but communicates only a binary output in biological decisions. Herein, we address the interface that determines fate outcomes. We provide an alternative hypothesis for the Notch pathway as a biological master switch that operates by induction of genetic noise and bistability in order to facilitate resolution of dichotomous fate outcomes in development. Graphical abstract

An observational cohort study to produce and evaluate an improved tool to screen older women with back pain for osteoporotic vertebral fractures (Vfrac): study protocol

Summary The aim of this study is to produce an easy to use checklist for general practitioners to complete whenever a woman aged over 65 years with back pain seeks healthcare. This checklist will produce a binary output to determine if the patient should have a radiograph to diagnose vertebral fracture. Purpose People with osteoporotic vertebral fractures are important to be identified as they are at relatively high risk of further fractures. Despite this, less than a third of people with osteoporotic vertebral fractures come to clinical attention due to various reasons including lack of clear triggers to identify who should have diagnostic spinal radiographs. This study aims to produce and evaluate a novel screening tool (Vfrac) for use in older women presenting with back pain in primary care based on clinical triggers and predictors identified previously. This tool will generate a binary output to determine if a radiograph is required. Methods The Vfrac study is a two-site, pragmatic, observational cohort study recruiting 1633 women aged over 65 years with self-reported back pain. Participants will be recruited from primary care in two sites. The Vfrac study will use data from two self-completed questionnaires, a simple physical examination, a lateral thoracic and lateral lumbar radiograph and information contained in medical records. Results The primary objective is to develop an easy-to-use clinical screening tool for identifying older women who are likely to have vertebral fractures. Conclusions This article describes the protocol of the Vfrac study; ISRCTN16550671.