NIFTy 3 – Numerical Information Field Theory: A Python Framework for Multicomponent Signal Inference on HPC Clusters

NIFTy , “Numerical Information Field Theory,” is a software framework designed to ease the development and implementation of field inference algorithms. Field equations are formulated independently of the underlying spatial geometry allowing the user to focus on the algorithmic design. Under the hood, NIFTy ensures that the discretization of the implemented equations is consistent. This enables the user to prototype an algorithm rapidly in 1D and then apply it to high‐dimensional real‐world problems. This paper introduces NIFTy  3, a major upgrade to the original NIFTy  framework. NIFTy  3 allows the user to run inference algorithms on massively parallel high performance computing clusters without changing the implementation of the field equations. It supports n‐dimensional Cartesian spaces, spherical spaces, power spaces, and product spaces as well as transforms to their harmonic counterparts. Furthermore, NIFTy  3 is able to handle non‐scalar fields, such as vector or tensor fields. The functionality and performance of the software package is demonstrated with example code, which implements a mock inference inspired by a real‐world algorithm from the realm of information field theory. NIFTy  3 is open‐source software available under the GNU General Public License v3 (GPL‐3) at https://gitlab.mpcdf.mpg.de/ift/NIFTy/tree/NIFTy_3 .     

Multistrain edge‐based compartmental model on networks

Multistrain diseases, which are infected through individual contacts, pose severe public health threat nowadays. In this paper, we build competitive and mutative two‐strain edge‐based compartmental models using probability generation function (PGF) and pair approximation (PA). Both of them are ordinary differential equations. Their basic reproduction numbers and final size formulas are explicitly derived. We show that the formula gives a unique positive final epidemic size when the reproduction number is larger than unity. We further consider competitive and mutative multistrain diseases spreading models and compute their basic reproduction numbers. We perform numerical simulations that show some dynamical properties of the competitive and mutative two‐strain models.     

Optimal packings of two to four equal circles on any flat torus

We find explicit formulas for the radii and locations of the circles in all the optimally dense packings of two, three or four equal circles on any flat torus, defined to be the quotient of the Euclidean plane by the lattice generated by two independent vectors. We prove the optimality of the arrangements using techniques from rigidity theory and topological graph theory.     

On the Motion of Substance in a Channel of a Network: Extended Model and New Classes of Probability Distributions

We discuss the motion of substance in a channel containing nodes of a network. Each node of the channel can exchange substance with: (i) neighboring nodes of the channel, (ii) network nodes which do not belong to the channel, and (iii) environment of the network. The new point in this study is that we assume possibility for exchange of substance among flows of substance between nodes of the channel and: (i) nodes that belong to the network but do not belong to the channel and (ii) environment of the network. This leads to an extension of the model of motion of substance and the extended model contains previous models as particular cases. We use a discrete-time model of motion of substance and consider a stationary regime of motion of substance in a channel containing a finite number of nodes. As results of the study, we obtain a class of probability distributions connected to the amount of substance in nodes of the channel. We prove that the obtained class of distributions contains all truncated discrete probability distributions of discrete random variable ω which can take values 0,1,⋯,N. Theory for the case of a channel containing infinite number of nodes is presented in Appendix A. The continuous version of the discussed discrete probability distributions is described in Appendix B. The discussed extended model and obtained results can be used for the study of phenomena that can be modeled by flows in networks: motion of resources, traffic flows, motion of migrants, etc.     

Quantum fractionalism: The Born rule as a consequence of the complex Pythagorean theorem

Everettian Quantum Mechanics, or the Many Worlds Interpretation, lacks an explanation for quantum probabilities. We show that the values given by the Born rule equal projection factors, describing the contraction of Lebesgue measures in orthogonal projections from the complex line of a quantum state to eigenspaces of an observable. Unit total probability corresponds to a complex Pythagorean theorem: the measure of a subset of the complex line is the sum of the measures of its projections on all eigenspaces.Postulating the existence of a continuum infinity of identical quantum universes, all with the same quasi-classical worlds, we show that projection factors give relative amounts of worlds. These appear as relative frequencies of results in quantum experiments, and play the role of probabilities in decisions and inference. This solves the probability problem of Everett's theory, allowing its preferred basis problem to be solved as well, and may help settle questions about the nature of probability.     

Protein-Mediated Suppression of Rolling Circle Amplification for Biosensing with an Aptamer-Containing DNA Primer

We report a method to detect proteins via suppression of rolling circle amplification (RCA) by using an appropriate aptamer as the linear primer (denoted as an aptaprimer) to initiate RCA. In the absence of a protein target, the aptaprimer is free to initiate RCA, which can produce long DNA products that are detected via binding of a fluorescent intercalating dye. Introduction of a target causes the primer region within the aptamer to become unavailable for binding to the circular template, inhibiting RCA. Using SYBR Gold or QuantiFluor dyes as fluorescent probes to bind to the RCA reaction product, it is possible to produce a generic protein-modulated RCA assay system that does not require fluorophore- or biotin-modified DNA species, substantially reducing complexity and cost of reagents. Based on this modulation of RCA, we demonstrate the ability to produce both solution and paper-based assays for rapid and quantitative detection of proteins including platelet derived growth factor and thrombin.     

Moderate Deviation for the Rightmost Position in a Branching Brownian Motion

We study the moderate deviation probability of the position of the rightmost particle in a branching Brownian motion and obtain its moderate deviation function. Firstly, Chauvin and Rouault studied the large deviation probability for the rightmost position in a branching Brownian motion. Recently, Derrida and Shiconsidered lower deviation for the same model. By contrast, Our main result is more extensive.     

Tutorial review on validation of liquid chromatography–mass spectrometry methods: Part I

This is the part I of a tutorial review intending to give an overview of the state of the art of method validation in liquid chromatography mass spectrometry (LC–MS) and discuss specific issues that arise with MS (and MS/MS) detection in LC (as opposed to the “conventional” detectors). The Part I briefly introduces the principles of operation of LC–MS (emphasizing the aspects important from the validation point of view, in particular the ionization process and ionization suppression/enhancement); reviews the main validation guideline documents and discusses in detail the following performance parameters: selectivity/specificity/identity, ruggedness/robustness, limit of detection, limit of quantification, decision limit and detection capability. With every method performance characteristic its essence and terminology are addressed, the current status of treating it is reviewed and recommendations are given, how to determine it, specifically in the case of LC–MS methods.     

Nucleic acid quantification using nicking–displacement,rolling circle amplification and bio-bar-code mediated triple-amplification

In the present study, an inductively-coupled plasma-mass spectrometry (ICP-MS)-based triple-amplification system, by combination of nicking–displacement, rolling circle amplification (RCA) and bio-bar-code probes, was fabricated for the detection of DNA target. By using this system, hepatitis B virus (HBV) DNA target down to 3.2 × 10⁻¹⁷ M was detected by DNA probes labeled with Au nanoparticles (AuNPs). Single nucleotide polymorphisms in genes can also be effectively discriminated. In addition, we proved that this strategy is capable of detecting the target in complicated biological samples and holds great potential application in biomedical research.