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Tyche Algorithm and Learning Elements Preferences
<p>This dataset contains the result of the survey to learning styles and their learning element preferences.</p> <p>The survey was executed in summer term of 2023 in German universities.</p> <p> </p> <p>The zip folder "implementation.zip" contains the code to the Tyche algorithm with some examples.</p> <p>The Python script runs with Python 3.10.5. Before executing, you need to install the packages of requirements.txt (pip install -r requirements.txt)</p> <p>For executing static and generic Tyche run "run_tyche.py"</p> <p> </p> <p>Refering to Data_local_view.xlsx</p> <p>Learning element01[1] means probability for first learning element after the lecture for Learning Goal.</p> <p>Coding for the numbers in brackets is the following:</p> <table> <tbody> <tr> <td>1</td> <td>Learning goal</td> </tr> <tr> <td>2</td> <td>Brief overview</td> </tr> <tr> <td>3</td> <td>Manuscript</td> </tr> <tr> <td>4</td> <td>Quiz</td> </tr> <tr> <td>5</td> <td>Exercise</td> </tr> <tr> <td>6</td> <td>Summary</td> </tr> <tr> <td>7</td> <td>Auditory additional material</td> </tr> <tr> <td>8</td> <td>Textual additional material</td> </tr> <tr> <td>9</td> <td>Visual additional material</td> </tr> </tbody> </table> <p> </p> <p>The presented work is supported by the ‘German Federal Ministry of Research, Technology and Space’ (BMFTR) through the granting of the funding project HASKI (FKZ: 16DHBKI035).</p>
Estimation of parasitic elements of silicon photomultipliers (SiPM)
<p>Project FleX-RAY employed photon counting capable photodiodes in order to capture light that was generated by the scintillation phenomenon, in plastic scintillating fibres. These special photodiodes are called Silicon Photomultipliers, or SiPMs. Electrical simulations were then carried out to evaluate different preamplifier architectures for SiPMs. For these simulations, we had to develop the electrical equivalent of an SiPM, however, many parameters that are necessary to develop an accurate model cannot be found in product datasheets or literature. This dataset contains electrical measurements and calculations that were conducted during the project, to estimate the values of various parasitic parameters of SiPMs available in the market.</p> <p>Specifically, the datasets contain Current vs Voltage (I-V) curves and Capacitance vs Electrical Conductance (Cp-G) curves that were used to extract the following parasitic parameters: quench resistance Rq, paralleled lumped capacitance Cm and conductance Gm. After the value of these parameters had been measured, capacitances Cq, Cd and Cg were mathematically derived.</p> <p>Two spreadsheets are included in this dataset:</p> <ol> <li>Spreadsheet titled "SiPM_I-V_curves.xlsx" contains measured Current vs Voltage (I-V) data, and derived Rq (quench resistance data), for the devices listed below.</li> <li>Spreadsheet titled "SiPMs_GvsCp.xls" contains the measured Conductance vs Parallel Capacitance (G-Cp) data, and derived Cq, Cd and Cg capacitance data, for the devices listed below.</li> </ol> <p>Devices under investigation: Hamamatsu SiPM models S12572-010, S12571-015, S13360-3075CS, S13360-3050CS, S13360-1375CS, S13360-1350CS and ON-semi SiPM models microFJ-30035, microFC-10035</p> <p>Measurement device(s)/board(s): Keysight Technologies 34401A Bench Digital Multimeter, Agilent 4294A Impedance analyzer, Generic bench-top power supplies</p> <p> </p> <p>This work was financed by the European Union's Horizon 2020 program under grant agreement No. 899634.</p>
Trace and rare-earth element composition of 2480 Ma detrital zircons in Proterozoic metapsammites from northwestern Arizona
<p>Detrital zircon grains in the ~1740-1750 Ma Vishnu Schist and similar rock units in northwestern Arizona consist of up to 30% grains dated by U-Pb isotopic analysis at 2470-2490 Ma. These zircon grains are distributed over ~40,000 km<sup>2 </sup>and define an age peak at 2480.0 ± 27.3 Ma (2SE). These grains have yielded unusually consistent <sup>207</sup>Pb/<sup>206</sup>Pb dates, with generally smaller analytical uncertainty and greater concordance to ideal U-Pb evolution than grains of other ages. A weighted mean age of 2480 ± 0.9 Ma (2SE) for this zircon population reflects consistent analytical results and high analytical precision but not the accuracy of the age. The source of these zircons has not been identified. To better characterize the unidentified source, we analyzed 45 of these grains for trace and rare-earth elements by laser-ablation mass spectrometry and scanned 16 grains with an electron microprobe to identify mineral inclusions. Mass spectrometer determinations of Sc/Yb and Nb/Sc support derivation from an oceanic-island igneous source. Electron microprobe scans revealed quartz in 5 of 16 grains, indicating a felsic source. The low variability in <sup>207</sup>Pb/<sup>206</sup>Pb dates and a generally linear relationship between U and Th support zircon derivation from a single igneous unit or closely related set of units without xenocrystic zircons. A literature search for other zircon populations with similar age and U/Th ratios identified ~2480 Ma zircons in a Mesoproterozoic(?) metapsammite and conglomerate in southwestern Montana. This sandstone was deposited near the margin of the Wyoming craton and contains almost entirely 2400-3600 Ma zircons, unlike zircon grains in Vishnu Schist which include a large population of 1730-1900 Ma zircons. From this relationship, we infer that the 2480 Ma zircons in both areas were derived from a source in the Wyoming craton. We conclude that the 2480 Ma Vishnu zircons were derived from a felsic batholith that formed above and from hotspot magma related to the ~2450-2480 Ma Matachewan Large Igneous Province, that this batholith formed by mixing between a mantle-derived hotspot magma and assimilated Archean continental crust, and that the source rock was emplaced during initial rifting between the Wyoming craton and the Superior province.</p>
Transposable element products, functions, and regulatory networks in Arabidopsis thaliana
<h1>README</h1> <p>This dataset includes the main outputs from the work titled <strong>Transposable element products, functions, and regulatory networks in <em>Arabidopsis thaliana</em>.</strong></p> <h2><strong>Summary</strong></h2> <p>Transposable elements (TEs) are DNA sequences with the ability to propagate themselves within and across genomes. Their mobilization is catalyzed by self-encoded factors, yet these factors have been poorly investigated due to difficulties in defining TE genes in genomes. Here, we leveraged extensive long- and short-read transcriptome data, together with structural predictions, transcription factor binding site identification, and transcriptional network analyses, to construct a comprehensive atlas of TE transcripts and TE-encoded products in the model organism <em>Arabidopsis thaliana</em>. We uncovered hundreds of transcriptionally competent TEs, each potentially encoding multiple proteins either through distinct genes, alternative splicing, or post-translational processing. Structural-based protein analyses revealed dozens of hitherto unidentified domains of unknown function, enabling us to predict proteins with multimerization and DNA binding domains forming macromolecular complexes involved in transposition. Furthermore, we demonstrate that TE expression is highly intertwined with the transcriptional network of cellular genes, and identified transcription factors and cis-regulatory elements associated with their coordinated expression during development or in response to environmental cues. This comprehensive atlas of TE-genes and TE-proteins provides a valuable resource for studying the mechanisms involved in transposition and their consequences for genome and organismal function.</p> <h2><strong>File description</strong></h2> <p>It includes the following data:</p> <ol> <li><code>annots/TE_Functional_Annotation.Borreda2024.gtf</code> - Annotation file including Arabidopsis TEs and TE-genes. TE-genes defined in our work are indicated in the 'Source' column of the gtf. TAIR10-defined TEs for whom we did not annotate new transcripts are also included.</li> <li><code>seqs</code> - This folders includes all the transcript sequences (cDNAs.tsv) and the first and longest ORFs found in each of them (prot.csv), which were used for further analyses. The specific copy, gene, isoform and, in the case of proteins, ORF, is indicated for each sequence.</li> <li><code>structures</code> - The zipped folder <code>full_length_prots_pdbs.zip</code> includes all the 3D structures from full-length TE proteins. Note that identical proteins, which would result in identical structures, have been collapsed to reduce the total dataset size; equivalences can be found in <code>identical_proteins</code>.</li> <li><code>structures/SD_Cluster_Functions.tsv</code> - We clustered all Structural Domains (SD) based on 3D similarity and assigned a function to each cluster based on the database hits. This table indicated, for each of these SDs, to which cluster it belongs, the superfamily, family and element containing it, the number of Conserved Domains included within it and the number of hits with resolved (retrieved from the RCSB-PDB database) or predicted (AlphaFold2) protein structures. The last column includes the putative function assigned to each cluster.</li> <li><code>coexpression</code> - Coexpressed genes were classiffied into modules using WGCNA. In the table <code>Gene_Modules.tsv</code> we include, for each gene and TE-gene (provided it has expression in at least one sample, see methods on the publication for details), the TE family and superfamily when applicable and the module to which it belongs. The modules were named based on the results of the GO enrichment analysis of the genes contained. The results of this GO enrichment are included in <code>GO_Enrichment.tsv</code>, where we include the main funciton of the associated GOs, the number of entries and TE-genes within the module, a list of GO terms enriched in that specific module and finally a list of TE families enriched in each module.</li> <li><code>dapseq</code> - We reanalized the DAP-seq dataset from O'Malley 2016, selecting only TFBS with a binding site within a DAP-seq peak. The list of filtered peaks we found is reported in <code>DAPseq_TFBS_Motifs.tsv</code>. The columns include the coordinates of the TFBS (which have been filtered to fall within a DAP-seq peak and include the TFBS motif), the strand of the motif, the score of the motif reported by FIMO, the motif sequence, the Sequence Read identified for the original DAP-seq data, and the family, name and gene of the TF associated with that specific peak.</li> </ol>
Exploring the preservation of a parasitic trace in decapod crustaceans using finite elements analysis
<p>The fossil record of parasitism is poorly understood, due largely to the scarcity of strong fossil evidence of parasites. Understanding the dynamics of preservation for fossil parasitic evidence is critical to contextualizing the fossil record of parasitism. Here, we present the first use of X-ray computed tomography (CT) scanning and finite elements analysis (FEA) to analyze the impact of a parasite-induced fossil trace on host preservation. Seven fossil and modern decapod crustacean specimens with branchial swellings attributed to an epicaridean isopod parasite were CT scanned and examined with FEA to assess differences in the magnitude and distribution of stress between normal and swollen branchial chambers. The results of the FEA show highly localized stress peaks in reaction to point forces, with higher peak stress on the swollen branchial chamber for all specimens, suggesting a possible shape-related decrease in the preservation potential of these parasitic swellings. Broader application of these methods as well as advances in the application of 3D data analysis in paleontology are critical to understanding the fossil record of parasitism and other poorly represented fossil groups.</p>
Alkyl lipid distribution, elemental composition and compound-specific 14C isotope composition in marine and terrestrial sedimentary archives from sub-Antarctic South Georgia
<p>The dataset comprises elemental data, alkyl lipid data and radiocarbon (14C) data that was obtained on sediment samples from sub-Antarctic South Georgia. The sediments were collected from a range of different sites, including lakes, peat deposits, a marine inlet and a fjord during RV Polarstern expedition PS81 in 2013. More details on the study sites, sampling and data evaluation can be found in Berg et al. (submitted manuscript to JGR Biogeochemistry).</p>
Finite element dataset and Artificial Neural Networks algorithms to predict the mechanical properties of innovative CLT
<p>This folder includes the data collected from the finite element simulations of the innovative CLT to compute its mechanical properties, the error of the closed-form solutions predicting the bending stiffness in the minor direction D22, the variation of the distance between the Reissner Mindlin and Bending Gradient theory in terms of spacing between lateral lamellas, the hyperparameters tuning of several Artificial Neural Networks algorithms with or without prior knowledge, the ML evaluations, the saved artificial neural network algorithms to predict each mechanical property of innovative CLT, and the ML application to use it.</p>
Collected data from finite element simulations to calculate the mechanical properties of innovative CLT using ABAQUS
<p>A dataset is collected from finite element computation using ABAQUS for different configurations of innovative CLT. In the dataset, we have the inputs (w, t1, t2, t3, t4, s, E_L, G_LZ, G_CZ) describing the microstructure of innovative CLT, and the elastic properties (Membrane stiffness: A11, A22, In-plane Poisson effect stiffness: A12, In-plane shear stiffness: A33, Bending stiffness: D11, D22, Out of plane Poisson effect stiffness: D12, Torsional stiffness: D33, out of plane Bending Gradient shear compliances: h11, h12, h16, h22, h26, h33, h34, h35, h44, h45, h55, h66) deriving from the FE computations. We have also the results of closed-form solutions that predicts these elastic properties of innovative CLT. </p>
Potentially harmful elements (As, Sb, Cd, Pb) in soil polluted by historical smelting operation in the Upper Silesian area (Southern Poland)
<p><span>Table S1: Elements concentration in the studies samples (ICP-MS); Ta<span>ble S2: Minerals and minerals phases in studied soils and slags; Table S3. Minerals and minerals phases in studied soils and slags.</span></span></p>
Fig. 6 in Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble
Fig. 6. Proposed Introgression Pathways identified using quartet asymmetry tests. Sixty-three quartets indicated significant deviation from expectations under incomplete lineage sorting. Pathways are identified by letters with number of supporting quartets in parentheses. Branch lengths are time-calibrated as in Fig. 1.
Fig. 5 in Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble
Fig. 5. Measures of population structure and diversity of the Nearctic Myotis species. (A) ASTRAL_I tree constructed from 2,615 UCE gene trees—dots indicate posterior probability (red> 0.9, blue = 1). (B) Principal component analysis of SNP loci from the UCE sequences—inset in B illustrates the amount of variance explained by PCs 1 to 11. (C) Map of sample collection locations. (D) Neighbor-joining tree constructed from SNPS. Colors in B–D are the same for each individual and are based on the first 3 components of the principal component analysis. Samples marked by * in A and D are individuals with discordant positions on the trees and are discussed further in the text.
Fig. 4 in Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble
Fig. 4. Measures of population structure and diversity of the Neotropical "ruber group." (A) ASTRAL_I tree constructed from 2,615 UCE gene trees—dots indicate posterior probability (red> 0.9, blue = 1). (B) Principal component analysis of SNP loci from the UCE sequences—inset in B illustrates the amount of variance explained by PCs 1 to 11. (C) Map of sample collection locations. (D) Neighbor-joining tree constructed from SNPs. Colors in B–D are the same for each individual and are based on the first 3 components of the principal component analysis.
Fig. 3 in Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble
Fig. 3. Measures of population structure and diversity of Neotropical "albescens group." (A) ASTRAL_I tree constructed from 2,615 UCE gene trees—dots indicate posterior probability (red> 0.9, blue = 1). (B) Principal component analysis of SNP loci from the UCE sequences—inset in B illustrates the amount of variance explained by PCs 1 to 11. (C) Map of sample collection locations. (D) Neighbor-joining tree constructed from SNPs. Colors in B–D are the same for each individual and are based on the first 3 components of the principal component analysis. Individuals indicated with colored symbols in A and D are individuals with discordant positions on the trees and are discussed further in the text.
Fig. 1 in Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble
Fig. 1. (A) Myotis ASTRAL_S species tree inferred from 2,615 UCE gene trees. Pie charts show the percentage of trees supporting each of 3 possible quartet topologies. All branches received posterior probabilities> 0.90. All others indicated with dots. Colored bars on the right of the tree show
Fig. 2 in Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble
Fig. 2. Comparison of tree conflict by marker for 3 broad phylogeographic Myotis groups: (A) Nearctic group; (B) Neotropical "albescens group"; (C) Neotropical "ruber group." This is a subset of individuals shown in Fig. 1A. For each group, the left tree displays the ASTRAL_I UCE phylogeny while the right displays the maximum likelihood Cyt b phylogeny. The same individuals are shown in each tree pair. Lines between trees denote notable topological differences between markers. Colors for highlighting by species are an approximated average color for that species as determined by the first 3 components of the PCAs shown in Figs. 3–5.
Hourly and daily values of meteorological elements from 40 meteorological stations located in Arizona (USA)
<p>The collection includes three text files (Arizona_meteo_hourly_01.txt; Arizona_meteo_hourly_02.txt; Arizona_meteo_daily.txt) with hourly and daily values of measurements from 40 meteorological stations located in Arizona (USA). The data was collected from September to November 2024 by Sylwester Wereski as a part of MINIATURA 5 "The occurrence of strong heat stress in hot and arid climate condition" (2021/05/X/ST10/00587), the research internship project at Arizona State University financed by the National Science Center in Poland. The source of data is website https://cales.arizona.edu/azmet/az-data.htm managed by AZMET (The Arizona Meteorological Network). The collection also includes a Readme.txt file, which contains a description of the location of the meteorological stations and the period of measurements conducted, as well as a description of meteorological variables.</p>
Negative Muon Elemental Spectroscopy Data
<p>Training and test data associated with the DNN exercise notebook from: <a href="https://github.com/mdi-group/iisc-ml-school">https://github.com/mdi-group/iisc-ml-school</a></p> <p>This work was supported by EPSRC project EP/Y000552/1 and Royal Society project IES\R3\223036.</p>
Investigating the cis-regulatory functions of transposable elements
<p>This repository contains the data and code associated with the article ‘<strong><span>Multi</span></strong><strong>-</strong><strong><span>omics analysis reveals critical cis-regulatory roles of transposable elements in livestock genomes</span></strong>'</p>
Electronic Supplement to: A Predictive Model for Divalent Element Partitioning between Clinopyroxene and Basaltic Melt and a Europium-in-Plagioclase-Clinopyroxene Oxybarometer for Cumulate Rocks
<p>Contents</p> <p>Supplementary Figures</p> <p>Supplementary Calculator Spreadsheet</p> <ul> <li>A calculator for divalent element partitioning between the clinopyroxene M2 site and silicate melt</li> <li>An fO2-, temperature- and composition- dependent clinopyroxene-melt Eu partition coefficient calculator for many samples, each at a single fO2</li> <li>An fO2-, temperature- and composition- dependent clinopyroxene-melt Eu partition coefficient calculator for a single sample at many fO2s</li> <li>A Eu-in-clinopyroxene-melt oxybarometer</li> <li>A Eu-in-plagioclase-clinopyroxene oxybarometer</li> </ul> <p>Supplementary Code</p> <ul> <li>A Eu-in-plagioclase-clinopyroxene oxybarometer</li> <li>A Monte Carlo-based fO2 uncertainty calculator</li> </ul>
Dataset for: Combined Ca, Sr isotope and trace element analyses of Late Cretaceous dinosaur teeth: assessing diet versus diagenesis
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