Electronically highly cubic conditions for Ru in alpha-RuCl3

We studied the local Ru 4d electronic structure of alpha-RuCl3 by means of polarization dependent x-ray absorption spectroscopy at the Ru-L2,3 edges. We observed a vanishingly small linear dichroism indicating that electronically the Ru 4d local symmetry is highly cubic. Using full multiplet cluster calculations we were able to reproduce the spectra excellently and to extract that the trigonal splitting of the t2g orbitals is -12 $\pm10$ meV, i.e. negligible as compared to the Ru 4d spin-orbit coupling constant. Consistent with our magnetic circular dichroism measurements, we found that the ratio of the orbital and spin moments is 2.0, the value expected for a Jeff = 1/2 ground state. We have thus shown that as far as the Ru 4d local properties are concerned, alpha-RuCl3 is an ideal candidate for the realization of Kitaev physics

Comparison of Multi-Sample Variant Calling Methods for Whole Genome Sequencing

Rapid advancement of next-generation sequencing (NGS) technologies has facilitated the search for genetic susceptibility factors that influence disease risk in the field of human genetics. In particular whole genome sequencing (WGS) has been used to obtain the most comprehensive genetic variation of an individual and perform detailed evaluation of all genetic variation. To this end, sophisticated methods to accurately call high-quality variants and genotypes simultaneously on a cohort of individuals from raw sequence data are required. On chromosome 22 of 818 WGS data from the Alzheimer's Disease Neuroimaging Initiative (ADNI), which is the largest WGS related to a single disease, we compared two multi-sample variant calling methods for the detection of single nucleotide variants (SNVs) and short insertions and deletions (indels) in WGS: (1) reduce the analysis-ready reads (BAM) file to a manageable size by keeping only essential information for variant calling ("REDUCE") and (2) call variants individually on each sample and then perform a joint genotyping analysis of the variant files produced for all samples in a cohort ("JOINT"). JOINT identified 515,210 SNVs and 60,042 indels, while REDUCE identified 358,303 SNVs and 52,855 indels. JOINT identified many more SNVs and indels compared to REDUCE. Both methods had concordance rate of 99.60% for SNVs and 99.06% for indels. For SNVs, evaluation with HumanOmni 2.5M genotyping arrays revealed a concordance rate of 99.68% for JOINT and 99.50% for REDUCE. REDUCE needed more computational time and memory compared to JOINT. Our findings indicate that the multi-sample variant calling method using the JOINT process is a promising strategy for the variant detection, which should facilitate our understanding of the underlying pathogenesis of human diseases

Artificial intelligence in digital pathology: a diagnostic test accuracy systematic review and meta-analysis

Ensuring diagnostic performance of AI models before clinical use is key to the safe and successful adoption of these technologies. Studies reporting AI applied to digital pathology images for diagnostic purposes have rapidly increased in number in recent years. The aim of this work is to provide an overview of the diagnostic accuracy of AI in digital pathology images from all areas of pathology. This systematic review and meta-analysis included diagnostic accuracy studies using any type of artificial intelligence applied to whole slide images (WSIs) in any disease type. The reference standard was diagnosis through histopathological assessment and / or immunohistochemistry. Searches were conducted in PubMed, EMBASE and CENTRAL in June 2022. We identified 2976 studies, of which 100 were included in the review and 48 in the full meta-analysis. Risk of bias and concerns of applicability were assessed using the QUADAS-2 tool. Data extraction was conducted by two investigators and meta-analysis was performed using a bivariate random effects model. 100 studies were identified for inclusion, equating to over 152,000 whole slide images (WSIs) and representing many disease types. Of these, 48 studies were included in the meta-analysis. These studies reported a mean sensitivity of 96.3% (CI 94.1-97.7) and mean specificity of 93.3% (CI 90.5-95.4) for AI. There was substantial heterogeneity in study design and all 100 studies identified for inclusion had at least one area at high or unclear risk of bias. This review provides a broad overview of AI performance across applications in whole slide imaging. However, there is huge variability in study design and available performance data, with details around the conduct of the study and make up of the datasets frequently missing. Overall, AI offers good accuracy when applied to WSIs but requires more rigorous evaluation of its performance.Comment: 26 pages, 5 figures, 8 tables + Supplementary material

Rich polymorphism of a rod-like liquid crystal (8CB) confined in two types of unidirectional nanopores

We present a neutron and X-rays scattering study of the phase transitions of 4-n-octyl-4'-cyanobiphenyl (8CB) confined in unidirectional nanopores of porous alumina and porous silicon (PSi) membranes with an average diameter of 30 nm. Spatial confinement reveals a rich polymorphism, with at least four different low temperature phases in addition to the smectic A phase. The structural study as a function of thermal treatments and conditions of spatial confinement allows us to get insights into the formation of these phases and their relative stability. It gives the first description of the complete phase behavior of 8CB confined in PSi and provides a direct comparison with results obtained in bulk conditions and in similar geometric conditions of confinement but with reduced quenched disorder effects using alumina anopore membranesComment: Accepted in EPJ E - Soft Matte

Magnonic Weyl states in Cu2OSeO3

The multiferroic ferrimagnet Cu$_2$OSeO$_3$ with a chiral crystal structure attracted a lot of recent attention due to the emergence of magnetic skyrmion order in this material. Here, the topological properties of its magnon excitations are systematically investigated by linear spin-wave theory and inelastic neutron scattering. When considering Heisenberg exchange interactions only, two degenerate Weyl magnon nodes with topological charges $\pm$2 are observed at high-symmetry points. Each Weyl point splits into two as the symmetry of the system is further reduced by including into consideration the nearest-neighbor Dzyaloshinsky-Moriya interaction, crucial for obtaining an accurate fit to the experimental spin-wave spectrum. The predicted topological properties are verified by surface state and Chern number analysis. Additionally, we predict that a measurable thermal Hall conductivity can be associated with the emergence of the Weyl points, the position of which can be tuned by changing the crystal symmetry of the material

Measurement of shower development and its Moli\`ere radius with a four-plane LumiCal test set-up

A prototype of a luminometer, designed for a future e+e- collider detector, and consisting at present of a four-plane module, was tested in the CERN PS accelerator T9 beam. The objective of this beam test was to demonstrate a multi-plane tungsten/silicon operation, to study the development of the electromagnetic shower and to compare it with MC simulations. The Moli\`ere radius has been determined to be 24.0 +/- 0.6 (stat.) +/- 1.5 (syst.) mm using a parametrization of the shower shape. Very good agreement was found between data and a detailed Geant4 simulation.Comment: Paper published in Eur. Phys. J., includes 25 figures and 3 Table

Performance of fully instrumented detector planes of the forward calorimeter of a Linear Collider detector

Detector-plane prototypes of the very forward calorimetry of a future detector at an e+e- collider have been built and their performance was measured in an electron beam. The detector plane comprises silicon or GaAs pad sensors, dedicated front-end and ADC ASICs, and an FPGA for data concentration. Measurements of the signal-to-noise ratio and the response as a function of the position of the sensor are presented. A deconvolution method is successfully applied, and a comparison of the measured shower shape as a function of the absorber depth with a Monte-Carlo simulation is given.Comment: 25 pages, 32 figures, revised version following comments from referee