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In this work, the image formation in a confocal laser scanning microscope (CLSM) is investigated for custom-made multi-cylinder phantoms. The cylinder structures were fabricated using 3D direct laser writing and consist of parallel cylinders with radii of 5 and 10 μm for the respective multi-cylinder phantom, with overall dimensions of about 200×200×200 μm3. Measurements were performed for different refractive index differences and by varying other parameters of the measurement system, such as pinhole size or numerical aperture (NA). For theoretical comparison, the confocal setup was implemented in an in-house developed tetrahedron-based and GPU-accelerated Monte Carlo (MC) software. The simulation results for a cylindrical single scatterer were first compared with the analytical solution of Maxwell’s equations in two dimensions for prior validation. Subsequently, the more complex multi-cylinder structures were simulated using the MC software and compared with the experimental results. For the largest refractive index difference, i.e., air as the surrounding medium, the simulated and measured data show a high degree of agreement, with all the key features of the CLSM image being reproduced by the simulation. Even with a significant reduction in the refractive index difference by the use of immersion oil to values as low as 0.005, a good agreement between simulation and measurement was observed, particularly with respect to the increase in penetration depth.

Manipulating the wavefront of coherent light incident on scattering media to enhance the imaging depth, sensitivity, and resolution is a common technique in biomedical applications. Local phase variations cause changes in the interference and can be used to create a focus inside or behind a scattering medium. We use wavefront shaping (WFS) to force constructive interference at an arbitrary location. The amount of light transmitted into a given region strongly depends on the scattering and absorption characteristics. These are described by their respective coefficients μs and μa and the scattering phase function. Controlling the scattering and absorption coefficients, we study the behavior of wavefront shaping and the achievable intensity enhancement behind volume scattering media with well-defined optical properties. The phantoms designed in this publication are made of epoxy resin. Into these epoxy matrices, specific amounts of scattering and absorbing particles, such as titanium dioxide pigments and molecular dyes, are mixed. The mixture obtained is filled into 3D-printed frames of various thicknesses. After a precise fabrication procedure, an integrating sphere-based setup characterizes the phantoms experimentally. It detects the total hemispherical transmission and reflection. Further theoretical characterization is performed with a newly developed hybrid PN method. This method senses the flux of light into a particular angular range at the lower boundary of a slab. The calculations are performed without suffering from ringing and fulfill the exact boundary conditions there. A decoupled two-path detection system allows for fast optimization as well as sensitive detection. The measurements yield results that agree well with the theoretically expected behavior.

Interference signals cause position errors and outages to global navigation satellite system (GNSS) receivers. However, to solve these problems, the interference source must be detected, classified, its purpose determined, and localized to eliminate it. Several interference monitoring solutions exist, but these are expensive, resulting in fewer nodes that may miss spatially sparse interference signals. This article introduces a low-cost commercial-off-the-shelf (COTS) GNSS interference monitoring, detection, and classification receiver. It employs machine learning (ML) on tailored signal pre-processing of the raw signal samples and GNSS measurements to facilitate a generalized, high-performance architecture that does not require human-in-the-loop (HIL) calibration. Therefore, the low-cost receivers with high performance can justify significantly more receivers being deployed, resulting in a significantly higher probability of intercept (POI). The architecture of the monitoring system is described in detail in this article, including an analysis of the energy consumption and optimization. Controlled interference scenarios demonstrate detection and classification capabilities exceeding conventional approaches. The ML results show that accurate and reliable detection and classification are possible with COTS hardware.

Transposable elements (TEs) are often the primary determinant of genome size differences among eukaryotes. In plants, the proliferation of TEs is countered through epigenetic silencing mechanisms that prevent mobility. Recent studies using the model plant Arabidopsis thaliana have revealed that methylated TE insertions are often associated with reduced expression of nearby genes, and these insertions may be subject to purifying selection due to this effect. Less is known about the genome-wide patterns of epigenetic silencing of TEs in other plant species. Here, we compare the 24-nt siRNA complement from A. thaliana and a closely related congener with a two-to threefold higher TE copy number, Arabidopsis lyrata. We show that TEs—particularly siRNA-targeted TEs—are associated with reduced gene expression within both species and also with gene expression differences between orthologs. In addition, A. lyrata TEs are targeted by a lower fraction of uniquely matching siRNAs, which are associated with more effective silencing of TE expression. Our results suggest that the efficacy of RNA-dlreeled DNA methylation silencing is lower in A. lyrata, a finding that may shed light on the causes of differential TE proliferation among species.

This study presents a simple and sustainable coating technology for the deposition of photocatalytic coatings based on titanium dioxide and geopolymers, which requires no thermal post-treatment. Titania powder P25, potassium silicate and a calcium aluminate-based hardener were dispersed in water and applied to aluminum substrates using a paintbrush, a roller and a spray gun. The coatings were air-dried for 12 h. The photocatalytic activities were tested via degradation of an aqueous methylene blue solution in a batch reactor under artificial UV-A light. The roller and the spray gun-based coatings yielded well-adhering coatings with high photocatalytic activity. Brushed coatings were inhomogeneous and unstable. The presented method of producing photocatalytic coatings is very simple to apply and does not require complex technologies or energy-intensive thermal treatments.

The reliable conversion and utilization of green hydrogen are often hindered by carbon monoxide (CO) impurities, which strongly poison conventional platinum catalysts in acidic media. To address this challenge, we developed PdPt alloys supported on reduced graphene oxide (PdPt/rGO) with controlled Pd:Pt ratios and investigated their activity toward the hydrogen oxidation (HOR) and hydrogen evolution reactions (HER). Structural analyses (PXRD, TEM, XPS, CO‐DRIFTS, H2‐D2 exchange) confirmed alloy formation, lattice strain, and electronic interactions between Pd and Pt, resulting in a downshifted d‐band center. These modifications weaken hydrogen and CO binding, leading to enhanced activity and CO tolerance. Among the series, Pd3Pt1/rGO showed the most balanced performance, delivering higher current densities and lower Tafel slopes than monometallic Pd/rGO and Pt/rGO, with activity comparable to commercial Pt/C. The results highlight that minimal Pt incorporation into Pd‐based catalysts effectively tunes the electronic structure, enabling reversible HOR/HER catalysis in acidic environments. This study provides a rational design approach for developing efficient, CO‐tolerant electrocatalysts to advance hydrogen energy technologies. PdPt alloys supported on reduced graphene oxide exhibit enhanced hydrogen oxidation and evolution activity in acidic media. Minimal Pt incorporation into Pd tunes the d‐band center and weakens hydrogen and CO binding, delivering superior activity and CO tolerance. This study highlights alloying as a practical strategy for designing cost‐effective, reversible hydrogen electrocatalysts. The schematic diagram illustrates a strategy for enhancing electrochemical catalyst performance toward CO‐tolerant HOR/HER applications

We present whole-genome assemblies of four divergent Arabidopsis thaliana strains that complement the 125-Mb reference genome sequence released a decade ago. Using a newly developed reference-guided approach, we assembled large contigs from 9 to 42 Gb of Illumina short-read data from the Landsberg erecta (Ler-1), C24, Bur-0, and Kro-0 strains, which have been sequenced as part of the 1,001 Genomes Project for this species. Using alignments against the reference sequence, we first reduced the complexity of the de novo assembly and later integrated reads without similarity to the reference sequence. As an example, half of the noncentromeric C24 genome was covered by scaffolds that are longer than 260 kb, with a maximum of 2.2 Mb. Moreover, over 96% of the reference genome was covered by the reference-guided assembly, compared with only 87% with a complete de novo assembly. Comparisons with 2 Mb of dideoxy sequence reveal that the per-base error rate of the reference-guided assemblies was below 1 in 10,000. Our assemblies provide a detailed, genomewide picture of large-scale differences between A. thaliana individuals, most of which are difficult to access with alignment-consensus methods only. We demonstrate their practical relevance in studying the expression differences of polymorphic genes and show how the analysis of sRNA sequencing data can lead to erroneous conclusions if aligned against the reference genome alone. Genome assemblies, raw reads, and further information are accessible through http://1001genomes.org/projects/assemblies.html.

The new research field of metagenomics is providing exciting insights into various, previously unclassified ecological systems. Next-generation sequencing technologies are producing a rapid increase of environmental data in public databases. There is great need for specialized software solutions and statistical methods for dealing with complex metagenome data sets. To facilitate the development and improvement of metagenomic tools and the planning of metagenomic projects, we introduce a sequencing simulator called MetaSim. Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a metagenome by specifying the number of genomes present at different levels of the NCBI taxonomy, and then to collect reads from the metagenome using a simulation of a number of different sequencing technologies. A population sampler optionally produces evolved sequences based on source genomes and a given evolutionary tree. MetaSim allows the user to simulate individual read datasets that can be used as standardized test scenarios for planning sequencing projects or for benchmarking metagenomic software.

The transition from vegetative to reproductive development is one of the most important phase changes in the plant life cycle. This step is controlled by various environmental signals that are integrated at the molecular level by so-called floral integrators. One such floral integrator in Arabidopsis (Arabidopsis thaliana) is the MADS domain transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). Despite extensive genetic studies, little is known about the transcriptional control of SOC1, and we are just starting to explore the network of genes under the direct control of SOC1 transcription factor complexes. Here, we show that several MADS domain proteins, including SOC1 heterodimers, are able to bind SOC1 regulatory sequences. Genome-wide target gene analysis by ChIP-seq confirmed the binding of SOC1 to its own locus and shows that it also binds to a plethora of flowering-time regulatory and floral homeotic genes. In turn, the encoded floral homeotic MADS domain proteins appear to bind SOC1 regulatory sequences. Subsequent in planta analyses revealed SOC1 repression by several floral homeotic MADS domain proteins, and we show that, mechanistically, this depends on the presence of the SOC1 protein. Together, our data show that SOC1 constitutes a major hub in the regulatory networks underlying floral timing and flower development and that these networks are composed of many positive and negative autoregulatory and feedback loops. The latter seems to be crucial for the generation of a robust flower-inducing signal, followed shortly after by repression of the SOC1 floral integrator.

Deciphering the mechanisms directing transcription factors (TFs) to specific genome regions is essential to understand and predict transcriptional regulation. TFs recognize short DNA motifs primarily through their DNA-binding domain. Some TFs also possess an oligomerization domain suspected to potentiate DNA binding but for which the genome-wide influence remains poorly understood. Here we focus on the LEAFY transcription factor, a master regulator of flower development in angiosperms. We have determined the crystal structure of its conserved amino-terminal domain, revealing an unanticipated Sterile Alpha Motif oligomerization domain. We show that this domain is essential to LEAFY floral function. Moreover, combined biochemical and genome-wide assays suggest that oligomerization is required for LEAFY to access regions with low-affinity binding sites or closed chromatin. This finding shows that domains that do not directly contact DNA can nevertheless have a profound impact on the DNA binding landscape of a TF.