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Chlamydiae are highly successful strictly intracellular bacteria associated with diverse eukaryotic hosts. Here we analysed metagenome-assembled genomes of the “Genomes from Earth’s Microbiomes” initiative from diverse environmental samples, which almost double the known phylogenetic diversity of the phylum. Our data and analyses provide an extended perspective of the variability of chlamydial biology and the ecology of this phylum of intracellular microbes.

We propose to continue our investigation of the structural anisotropies in bulk metallic glasses with X-ray nano-diffraction. Our initial experiment at ID16B revealed large and unexpected structural anisotropies discovered by analyzing the full 2D diffraction pattern. The patterns showed large intensity variations as a function of the azimuthal angle. The results of the studies we propose on several samples with different growth conditions and degrees of stability can inform the relationship between the observed anisotropies and important properties of metallic glasses, pointing to the need to have structural information beyond the density-density pair distribution function. Further, these studies may provide new information relevant to the glass transition, a long-standing open question in condensed matter physics.

The data set includes eddy-covariance measurements collected during two field campaigns (2017–2018 and 2019–2020) carried out in the Schirmacher oasis, East Antarctica (70° 45′ S, 11° 44′ E). During the campaigns, the integrated CO2 and H2O open-path gas analyzer and 3-D sonic anemometer Irgason by Campbell Scientific (the serial number 1243) was operated on the shore of two glacial lakes. In the first experiment, the Irgason was deployed on the north-west shore of Lake Zub/Priyadarshini at a distance of 10 m from the coast used from 01.01.2018 to 07.02.2018. The instrument was placed on the aluminium tripod on the height of 2 m, and its sensor was directed toward 137° south-eastwards (SE). The second experiment lasted from 07.12.2019 to 13.01.2020; the Irgason was deployed at a distance of 10 m from the shore of Lake Glubokoe at a height of 1.8 m and the sensor was directed toward 144° south-eastwards (SE). The data are stored in the datafiles with the format given in Irgason_output.pdf; the raw data are packed into the *.dat files (one per day) and then compressed (bz2). The calibration of the Irgason was done 21.08.2017 and 13.11.2019 in the lab of the Finnish Meteorological Institute with standard zero-and-span procedure, and then the instrument was adjusted accordingly. The Irgason joined the inter-calibration campaign carried out in October 2018 in Lake Alqueva (Portugal). The work has received financial support from the Academy of Finland (contract number 304345, PI Timo Vihma); the logistic support of the field campaigns provided by the Finnish Antarctic Research Program and the Russian Antarctic Expedition.

Genome sequence and annotation of Fragaria vesca cv. Reine des Vallées In order to generate a reference genome for Fragaria vesca cv. Reine des Vallées, we used MinIon long-read sequencing data to substitute the F. vesca genome v.4.0.a2 genome. The detailed method used to obtain these results were the following: Genome sequencing and assembly NIL Fb2 Genomic DNA from strawberry plants was extracted by a Hexadecyltrimethylammonium bromide (Cetrimonium bromide, CTAB) modified protocol (Healey, Furtado, Cooper, & Henry, 2014) and purified with Agencourt AMPure XP beads (cat# A63880). Long-read sequencing was performed for the genome assembly; Genomic DNA by Ligation (Oxford Nanopore, cat# SQK-LSK109) library was prepared as described by the manufacturer and sequenced on a MinION for 72 h (Oxford Nanopore). Reference genome polishing Reads obtained from nanopore were filtered with Filtlong v0.2.1 (https://github.com/rrwick/Filtlong) using --min_mean_q 80 and --min_length 200. Cleaned reads were then aligned to the most recent version of the F. vesca genome v4.0.a2, downloaded from the Genome Database for Rosaceae (GDR) (https://www.rosaceae.org/species/fragaria_vesca/genome_v4.0.a2), using minimap2 v2.21 (H. Li, 2018) with parameters -aLx map-ont --MD -Y. The generated BAM file was then sorted and indexed with samtools v1.11 (H. Li et al., 2009). We used mosdepth v0.3.1 (Pedersen & Quinlan, 2018) to verify that coverage on chromosomic scaffolds was over 50 X. Sniffles v1.0.12a (Sedlazeck et al., 2018) with parameters -s 10 -r 1000 -q 20 --genotype -l 30 -d 1000 was used to detect structural variations larger than 30 bp. The VCF files obtained from Sniffles was sorted and filtered with BCFtools v1.14 (Danecek et al., 2021) to keep only structural variants (SV) with smaller than 200,00 bp (we observed that larger SV were most of the time false positive caused by misalignments in regions with gaps or Ns), supported by 10 or more reads and with allelic frequencies above 0.8 (we were interested in homozygous changes). The complete filtering command used is “bcftools view -q 0.8 -Oz -i '(SVTYPE = "DUP" || SVTYPE = "INS" || SVTYPE = "DEL" || SVTYPE = "TRA" || SVTYPE = "INV" || SVTYPE = "INVDUP") && %FILTER = "PASS" && FMT/DV>9 && SVLEN>29 && SVLEN<200000' “ From the VCF listing all the structural variants that we detected in our F. vesca accession, we generated a substituted genome version based on the reference F. vesca genome v.4.0.a2. The reference genome was first indexed with samtools faidx v1.11(Danecek et al., 2021) and a sequence dictionary was generated with Picard CreateSequenceDictionary v2.25.6 (https://broadinstitute.github.io/picard). The VCF containing the SV produced from our Nanopore sequencing was also indexed with gatk (Van der Auwera GA & O'Connor BD, 2020) IndexFeatureFile v4.2.0.0 (https://gatk.broadinstitute.org/hc/en-us/articles/360037262651-IndexFeatureFile). FastaAlternateReferenceMaker v4.2.0.0 (https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker) was then run with the reference genome and the VCF file to generate a substituted genome representative of our Fragaria accession. As substituting our genome with the detected structural variants changes genomic coordinates, we also corrected the public GFF genome annotation of F. vesca (Y, Pi, Gao, Liu, & Kang, 2019) using liftoff v1.6.1 (Shumate & Salzberg, 2021). Liftoff also detects and annotates duplications within the substituted genome. Transposable elements annotation was carried out using the EDTA transposable element annotation pipeline v. 1.9.6 (S. Ou et al., 2019) on the substituted genome using default parameters. Differentially methylated regions The file Stress_vs_control_DMRs.zip file contains the DMRs that were called using the reads submitted to ENA (ERP135585) and obtained as follows: First, bedGraph files from wgbs pipeline were pre-filtered for a minimum coverage of 5 reads using awk command. These output files were then used as input for the EpiDiverse/dmr bioinformatics analysis pipeline for non-model plant species to define DMRs (Nunn et al., 2021) with default parameters (minimum coverage threshold 5; maximum q-value 0.05; minimum differential methylation level 10%; 10 as minimum number of Cs; Minimum distance (bp) between Cs that are not to be considered as part of the same DMR is 146 bp). The pipeline uses metilene v.0.2.6.1 (https://www.bioinf.uni-leipzig.de/Software/metilene/) for pairwise comparison between groups and R-packages ggplot2 v.3.3.5 and gplots v.3.1.1, for visualization results (Fig. S1). Based on our F. vesca genome transcript annotation and methylation data (overlapped regions with DNA methylation cytosines and DMRs), we detected the methylated genes, promoters, 3’ UTRs, 5’UTR and transposable elements in strawberry. Global DNA methylation and DMR plots were performed with R-package ggplot2. Gene analyses by methylation patterns and analysis of per-family TE DNA methylation profiles were performed with deepTools v.3.5.0 (Ramírez et al., 2014). DMRs comparison between treatments were done by the Venn diagram v.1.7.0 R-package. We produced several genome browsers tracks with DMRs that we integrated in our local instance of JBrowse available at the following url: https://jbrowse.agroscope.info/jbrowse/?data=fragaria_sub

Masonry vaults play a much relevant role in the seismic response of heritage masonry buildings, ranging from housing to the greatest cathedrals. Acting as both a ceiling and a structural horizontal diaphragm with significant mass, their mechanical behaviour affects the overall seismic response of buildings, in terms of strength, stiffness, and ductility. Moreover, local damage and collapse of vaults may produce significant losses in terms of cultural assets and casualties. In spite of the importance of this topic, the evaluation of the complex three-dimensional behaviour of vaults is still an important challenge for researchers. The main objectives of the present research project are: 1) to better understand the seismic behaviour of masonry cross vaults by means of shaking table tests on both full-scale and small-scale models; 2) to assess the capability of different modelling/analysis approaches to predict the seismic response of these masonry structures. In particular, three sets of shaking table tests are planned: a. Tests on a 1:1 scale model of a brick unreinforced masonry cross vault: to investigate the behaviour of brick masonry cross vaults under different seismic inputs, in terms of damage, displacement capacity and peak acceleration. b. Tests on a 1:1 scale model of a brick reinforced masonry cross vault: to evaluate the effectiveness of reinforcing techniques to repair the vaults tested in a). In addition to the experimental tests, a blind prediction competition is performed to assess the efficacy of different modelling strategies and analysis techniques. The final aims are to improve the safety assessment procedures proposed for historic masonry buildings in Eurocode 8.3 and to provide better seismic assessment techniques and strengthening measures. {"references": ["Bianchini, Nicoletta, Nuno Mendes, Chiara Calderini, and Paulo B Louren\u00e7o. 2023. \"Modelling of the Dynamic Response of a Reduced Scale Dry Joints Groin Vault.\" Journal of Building Engineering 66. https://doi.org/10.1016/j.jobe.2023.105826.", "Bianchini, Nicoletta, Nuno Mendes, Paulo Xavier Candeias, Chiara Calderini, Michela Rossi, and Paulo B. Louren\u00e7o. 2022. \"Seismic Response of a Small-Scale Masonry Groin Vault : Experimental Investigation by Performing Quasi-Static and Shake Table Tests.\" Bulletin of Earthquake Engineering, 1\u201323. https://doi.org/10.1007/s10518-021-01280-0.", "Bianchini, Nicoletta, Angelo Gaetani, Nuno Mendes, and Paulo B Louren\u00e7o. 2022. \"Experimental Behaviour of Masonry : Static and Dynamic Behaviour of Arches and Vaults.\" In From Corbel Arches to Double Curvature Vaults Analysis, Conservation and Restoration of Architectural Heritage Masonry Structures, edited by Gabriele Milani and Vasilis Sarhosis, Research f, 79\u2013121. Cham: Springer International Publishing. https://doi.org/https://doi.org/10.1007/978-3-031-12873-8_5.", "Bianchini, Nicoletta, Nuno Mendes, Paulo B. Louren\u00e7o, Chiara Calderini, and Michela Rossi. 2019. \"Seismic Assessment of Masonry Cross Vaults through Numerical Nonlinear Static and Dynamic Analysis.\" In COMPDYN 2019 7th ECCOMAS Thematic Conference on Computational Methods in Structural Dynamics and Earthquake Engineering, edited by M. Papadrakakis and M. Fragiadakis, 600\u2013612. Crete, Greece. https://doi.org/10.7712/120119.6942.18709."]}

This data set contains: - Averaged temperature measurements data - Species concentrations measurements in the exhausted gas - Ensemble-averaged OH* and CH* radicals chemiluminescence spatially resolved intensity values The furnace is fired using a 20 kW capacity recuperative commercial flame/FLOX® burner (REKUMAT M150) of WS make. The following fuel mixtures were tested: - Fuel mixtures of CH4/H2 - Fuel mixtures of NH3/H2 - Fuel mixtures of CH3OCH3/CH4 and CH3OCH3/H2 {"references": ["10.1016/j.ijhydene.2021.07.161", "10.1016/j.ijhydene.2022.10.104", "10.3389/fenrg.2020.597655"]}

Data was collected from 5246 consumers responsible for buying food in their homes in 5 EU countries (Germany, Netherlands, Italy, Czech Republic, and Spain). The collected information corresponds to 1) socio-demographic information, 2) t consumer’s purchase intention and willingness to pay for beef obtained by circular farming (DCE), 3) and variables related to the components of the planned behaviour theory (social norms, environmental attitudes, consumer´ perceived behavioural control and frequency of consumption, and general sustainable behaviour).

Dataset used for the figures presented in the paper "Design and optimization of a Chloride Molten Salt Fast Reactor" for the ICAPP2023 conference

This resource is a dataset of routinely acquired maternal-fetal screening ultrasound images collected in five centers of five countries in Africa (Malawi, Egypt, Uganda, Ghana and Algeria) that is associated to the journal article Sendra-Bacells et al. "Generalisability of fetal ultrasound deep learning models to low-resource imaging settings in five African countries", Scientific Reports. The images correspond to the four most common fetal planes: abdomen, brain, femur and thorax. A CSV file is provided where image filenames are associated to plane types and patient number as well as the partitioning in training and testing splits as used in the associated publication. This work also received funding from the Spanish Ministry of Science, Innovation and Universities under grant agreement RTI2018-099898-B-I00. Additionally, the research leading to these results has received funding from Cerebra Foundation for the Brain Injured Child (Carmarthen, Wales, UK).

Data and code for the paper "Representing storylines with causal networks to support decision making: framework and example", along with the Shiny webapp code accompanying the paper. The paper has been submitted to the journal of Climate Risk Management and is currently under review.