TiDeTree: a Bayesian phylogenetic framework to estimate single-cell trees and population dynamic parameters from genetic lineage tracing data.

The development of organisms and tissues is dictated by an elaborate balance between cell division, apoptosis and differentiation: the cell population dynamics. To quantify these dynamics, we propose a phylodynamic inference approach based on single-cell lineage recorder data. We developed a Bayesian phylogenetic framework-time-scaled developmental trees (TiDeTree)-that uses lineage recorder data to estimate time-scaled single-cell trees. By implementing TiDeTree within BEAST 2, we enable joint inference of the time-scaled trees and the cell population dynamics. We validated TiDeTree using simulations and showed that performance further improves when including multiple independent sources of information into the inference, such as frequencies of editing outcomes or experimental replicates. We benchmarked TiDeTree against state-of-the-art methods and show comparable performance in terms of tree topology, plus direct assessment of uncertainty and co-estimation of additional parameters. To demonstrate TiDeTree's use in practice, we analysed a public dataset containing lineage data from approximately 100 stem cell colonies. We estimated a time-scaled phylogeny for each colony; as well as the cell division and apoptosis rates underlying the growth dynamics of all colonies. We envision that TiDeTree will find broad application in the analysis of single-cell lineage tracing data, which will improve our understanding of cellular processes during development.

Automated spray coating process for the fabrication of large-area artificial opals on textured substrates.

3D photonic crystals, such as opals, have been shown to have a high potential to increase the efficiency of solar cells by enabling advanced light management concepts. However, methods which comply with the demands of the photovoltaic industry for integration of these structures, i. e. the fabrication in a low-cost, fast, and large-scale manner, are missing up to now. In this work, we present the spray coating of a colloidal suspension on textured substrates and subsequent drying. We fabricated opaline films of much larger lateral dimensions and in much shorter times than what is possible using conventional opal fabrication methods.

Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data.

Genome sequences from evolving infectious pathogens allow quantification of case introductions and local transmission dynamics. We sequenced 11,357 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Switzerland in 2020-the sixth largest effort globally. Using a representative subset of these data, we estimated viral introductions to Switzerland and their persistence over the course of 2020. We contrasted these estimates with simple null models representing the absence of certain public health measures. We show that Switzerland's border closures decoupled case introductions from incidence in neighboring countries. Under a simple model, we estimate an 86 to 98% reduction in introductions during Switzerland's strictest border closures. Furthermore, the Swiss 2020 partial lockdown roughly halved the time for sampled introductions to die out. Last, we quantified local transmission dynamics once introductions into Switzerland occurred using a phylodynamic model. We found that transmission slowed 35 to 63% upon outbreak detection in summer 2020 but not in fall. This finding may indicate successful contact tracing over summer before overburdening in fall. The study highlights the added value of genome sequencing data for understanding transmission dynamics.

Radiation Hardness and Self-Healing of Perovskite Solar Cells.

The radiation hardness of CH3 NH3 PbI3 -based solar cells is evaluated from in situ measurements during high-energy proton irradiation. These organic-inorganic perovskites exhibit radiation hardness and withstand proton doses that exceed the damage threshold of crystalline silicon by almost 3 orders of magnitude. Moreover, after termination of the proton irradiation, a self-healing process of the solar cells commences.