Assessment of real-time bioaerosol particle counters using reference chamber experiments

This study presents the first reference calibrations of three commercially available bioaerosol detectors. The Droplet Measurement Technologies WIBS-NEO (new version of the wideband integrated bioaerosol spectrometer), Plair Rapid-E, and Swisens Poleno were compared with a primary standard for particle number concentrations at the Federal Institute for Metrology (METAS). Polystyrene (PSL) spheres were used to assess absolute particle counts for diameters from 0.5 to 10 µm. For the three devices, counting efficiency was found to be strongly dependent on particle size. The results confirm the expected detection range for which the instruments were designed. While the WIBS-NEO achieves its highest efficiency with smaller particles, e.g. 90 % for 0.9 µm diameter, the Plair Rapid-E performs best for larger particles, with an efficiency of 58 % for particles with a diameter of 10 µm. The Swisens Poleno is also designed for larger particles but operates well from 2 µm. However, the exact counting efficiency of the Poleno could not be evaluated as the cut-off diameter range of the integrated concentrator unit was not completely covered. In further experiments, three different types of fluorescent particles were tested to investigate the fluorescent detection capabilities of the Plair Rapid-E and the Swisens Poleno. Both instruments showed good agreement with the reference data. While the challenge to produce known concentrations of larger particles above 10 µm or even fresh pollen particles remains, the approach presented in this paper provides a potential standardised validation method that can be used to assess counting efficiency and fluorescence measurements of automatic bioaerosol monitoring devices.

Analog pile-up circuit technique using a single capacitor for the readout of Skipper-CCD detectors

With Skipper-CCD detectors it is possible to take multiple samples of the charge packet collected on each pixel. After averaging the samples, the noise can be extremely reduced allowing the exact counting of electrons per pixel. In this work we present an analog circuit that, with a minimum number of components, applies a double slope integration (DSI) and at the same time averages the multiple samples, producing at its output the pixel value with sub-electron noise. For this purpose, we introduce the technique of using the DSI integrator capacitor to add the skipper samples. An experimental verification using discrete components is presented, together with an analysis of its noise sources and limitations. After averaging 400 samples it was possible to reach a readout noise of 0.18 e- rms/pix, comparable to other available readout systems. Due to its simplicity and significant reduction of the sampling requirements, this circuit technique is of particular interest in particle experiments and cameras with a high density of Skipper-CCDs.

On The Exact Counting of Tree-Child Networks

The combinatorial study of phylogenetic networks has attracted much attention in recent times. In particular, one class of them, the so-called tree-child networks, are becoming the most prominent ones. However, their combinatorial properties are largely unknown. In this paper we address the problem of exactly counting them. We conjecture a bijection with a certain class of words, and from this assumption a simple recurrence formula arises. It is able to determine the number of all subclasses, as well as a direct formula, a simple enumeration procedure and precise asympotics. Our results coincide with all currently proved formulas for particular subclasses of tree-child networks, as well as with numerical results obtained for small networks. Since, as we will show, working with words greatly simplies the problem, we expect to contribute to further combinatoric characterizations of this class of networks.

Assessment of Real-time Bioaerosol Particle Counters using Reference Chamber Experiments

This study presents the first reference calibrations of three commercially available bioaerosol detectors. The Droplet Measurement Technologies WIBS-NEO, Plair Rapid-E, and Swisens Poleno were compared with a primary standard for particle number concentrations at the Federal Institute for Metrology METAS. Polystyrene (PSL) spheres were used to assess absolute particle counts for diameters from 0.5 μm to 10 μm. For the three devices, counting efficiency was found to be strongly dependent on particle size. The results confirm the expected detection range for which the instruments were designed. While the WIBS-NEO achieves its highest efficiency at smaller particles, e.g. 90 % for 0.9 μm diameter, the Plair Rapid-E performs best for larger particles, with an efficiency of 58 % for particles with a diameter of 10 μm. The Swisens Poleno is also designed for larger particles, but operates well from 2 μm. However, the exact counting efficiency of the Poleno could not be evaluated as the cut-off diameter range of the integrated concentrator unit was not completely covered. In further experiments, three different types of fluorescent particles were tested to investigate the fluorescent detection capabilities of the Plair Rapid-E and the Swisens Poleno. Both instruments showed good agreement with the reference data. While the challenge to produce known concentrations of larger particles above 10 μm or even fresh pollen particles remain, the approach presented in this paper provides a potential standardised validation method that can be used to assess counting efficiency and fluorescence measurements of automatic bioaerosol monitoring devices.

Mapping yeast mitotic 5’ resection at base resolution reveals the sequence and positional dependence of nucleases in vivo

Resection of the 5’-terminated strand at DNA double strand breaks (DSBs) is the critical regulated step in the transition to homologous recombination. Biochemical and genetic studies have led to a multi-step model of DSB resection in which endonucleolytic cleavage mediated by Mre11 in partnership with Sae2 is coupled with exonucleolytic cleavage mediated by redundant pathways catalyzed by Exo1 and Sgs1/Dna2. These models have not been well tested at mitotic DSBs in vivo because most methods commonly used to monitor resection cannot precisely map early cleavage events. Here we report resection monitoring with next-generation sequencing in which unique molecular identifiers allow exact counting of cleaved 5’ ends at base pair resolution. Mutant strains, including exo1Δ, mre11-H125N, exo1Δ and exo1Δ sgs1Δ, revealed a major Mre11-dependent cleavage position 60 to 70 bp from the DSB end whose exact position depended on local sequence and tracked an apparent motif. They further revealed an Exo1-dependent pause point approximately 200 bp from the DSB. Suppressing resection extension in exo1Δ sgs1Δ yeast exposed a footprint of regions where cleavage was restricted within 119 bp of the DSB and near the Exo1 pause point and where it was much less restrained. These results provide detailed in vivo support of prevailing models of DSB resection and extend them to show the combined influence of sequence specificity and access restrictions on Mre11 and Exo1 nucleases.

Chapter 26. Approximate Model Counting

Model counting, or counting solutions of a set of constraints, is a fundamental problem in Computer Science with diverse applications. Since exact counting is computationally hard (#P complete), approximate counting techniques have received much attention over the past few decades. In this chapter, we focus on counting models of propositional formulas, and discuss in detail universal-hashing based approximate counting, which has emerged as the predominant paradigm for state-of-the-art approximate model counters. These counters are randomized algorithms that exploit properties of universal hash functions to provide rigorous approximation guarantees, while piggybacking on impressive advances in propositional satisfiability solving to scale up to problem instances with a million variables. We elaborate on various choices in designing such approximate counters and the implications of these choices. We also discuss variants of approximate model counting, such as DNF counting and weighted counting.

Empirical Bounds on Linear Regions of Deep Rectifier Networks

We can compare the expressiveness of neural networks that use rectified linear units (ReLUs) by the number of linear regions, which reflect the number of pieces of the piecewise linear functions modeled by such networks. However, enumerating these regions is prohibitive and the known analytical bounds are identical for networks with same dimensions. In this work, we approximate the number of linear regions through empirical bounds based on features of the trained network and probabilistic inference. Our first contribution is a method to sample the activation patterns defined by ReLUs using universal hash functions. This method is based on a Mixed-Integer Linear Programming (MILP) formulation of the network and an algorithm for probabilistic lower bounds of MILP solution sets that we call MIPBound, which is considerably faster than exact counting and reaches values in similar orders of magnitude. Our second contribution is a tighter activation-based bound for the maximum number of linear regions, which is particularly stronger in networks with narrow layers. Combined, these bounds yield a fast proxy for the number of linear regions of a deep neural network.