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2,960 results for “elements”
Data for: Gene tree estimation error with ultraconserved elements: An empirical study on Pseudapis bees
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Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts
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Elemental composition, respiration, and excretion measurements of pteropods collected from the PAL LTER research cruises along the Western Antarctic Peninsula 2017-2019.
Pteropods (pelagic snails) are abundant zooplankton in the Southern Ocean where they are important grazers of phytoplankton, prey for higher trophic levels, and sensitive to environmental change. In this study, the effects of warming seawater temperatures and shifting food availability on Limacina helicina antarctica metabolism (respiration and excretion) were determined by conducting shipboard experiments that exposed pteropods to a range of temperatures and phytoplankton (food) concentrations. Pteropods and all other macrozooplankton were collected with a 2 m square frame Metro net (700 µm mesh), towed obliquely to depths up to 120 m (Ross et al., 2008; Steinberg et al., 2015), or with shallower (0-50 m), vertical tows if pteropods were very abundant. Pteropods were exposed to varying temperature and food conditions for 12 hours and respiration and excretion were measured. Incubations were also conducted with non-shelled pteropod species and shelled pteropod, Clio pyramidata, measuring pteropod respiration under in situ conditions. Finally, a CO2 perturbation experiment measuring L. h. antarctica metabolism (respiration and excretion) under pre-industrial and elevated dissolved CO2 conditions at ambient temperature in filtered seawater (no food), during the 2018 PAL LTER research cruise. Results reveal the metabolic response of pteropods to ocean variability, increase our understanding of the role of zooplankton in biogeochemical cycles, and help predict future responses to climate change.
IODP Expedition 361 Elemental analysis (CHNS)
<p>Fundamental elemental component (total carbon, hydrogen, nitrogen, and sulfur) fluctuations help define the origin, depositional environment, and diagenetic alteration of source materials. To determine C, H, N, and S, solid samples are reacted with a catalyst, separated by chromatography, and detected by thermal conductivity on a FlashEA 1112 CHNS elemental analyzer. Organic carbon can be directly measured on the elemental analyzer by acidification of the sample to drive off carbonate as carbon dioxide before analyzing. Total organic carbon on this report is measured rather than calculated.</p>
data sets for "Ultra-Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea)"
<p>data sets used in :</p> <p>Cruaud A, Delvare G, Nidelet S, Sauné L, Ratnasingham S, Chartois M, Blaimer BB, Gates M, Brady SG, Faure S, van Noort S, Rossi J-P, and Rasplus J-Y. in press. Ultra-Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea). Cladistics.</p> <p>1) morphological matrix (matrix_morphology_chalcididae_cladistics2020.nex) : Further details on characters and character states as well as illustrations can be found in the manuscript.</p> <p>2) concatenated UCE data set (merge_UCEs_chalcididae_cladistics2020.phy)</p> <p>3) all phylogenetic trees (morphology, UCEs, subset of UCEs; see paper for further details)</p> <p>4) a mesquite file with mapping of morphological characters on alternative UCE trees and the MJ consensus tree of the morphological analysis (mesquite_trees_and_morphological_transformations_chalcididae_cladistics2020.nex)</p>
IODP Expedition 362 Elemental analysis (CHNS)
<p>Fundamental elemental component (total carbon, hydrogen, nitrogen, and sulfur) fluctuations help define the origin, depositional environment, and diagenetic alteration of source materials. To determine C, H, N, and S, solid samples are reacted with a catalyst, separated by chromatography, and detected by thermal conductivity on a FlashEA 1112 CHNS elemental analyzer. Organic carbon can be directly measured on the elemental analyzer by acidification of the sample to drive off carbonate as carbon dioxide before analyzing. Total organic carbon on this report is measured rather than calculated.</p>
IODP Expedition 362 ICP-AES elemental analysis (interstitial water)
<p>Elemental concentration in interstitial water samples was measured by inductively coupled plasma - atomic emission spectroscopy (ICP-AES). Data are presented by element-wavelength pair (e.g., more than one calcium line may be reported). Elemental lines for which data do not exist for a particular expedition will not appear.</p>
IODP Expedition 361 ICP-AES elemental analysis (solids)
<p>Elemental contents in hard rock and sediment samples was measured by inductively coupled plasma - atomic emission spectrocopy (ICP-AES). Data are presented by element-wavelength pair (e.g., more than one calcium line may be reported). Elemental lines for which data do not exist for a particular expedition will not appear.</p>
Raw data on Elements of eating pattern and intensity of dysmenorrhea – cross sectional study in sample of Polish women
<p>Raw data used in the analysis on the paper "Elements of eating pattern and intensity of dysmenorrhea - a cross-sectional study in sample of Polish women".</p>
Chemical characteristics of the assigned elemental formulas from the FT-ICR MS data of aerosol-derived organic matter simultaneously collected in Beijing, China and Gwangju, Korea in January 2018
<p>In this study, ambient fine particles (PM2.5) were simultaneously collected in two urban cities in China and Korea (Beijing and Gwangju, respectively) in January 2018. Comprehensive compositional analysis of the organic matter (OM) samples, extracted using dichloromethane, was performed on a 15 Tesla Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with an atmospheric pressure photoionization (APPI) interface in positive ion mode. Analysis of the nonpolar and semipolar OM using APPI FT-ICR MS revealed that CHO and CHON accounted for more than 90% of the total intensity of the OM peaks. Higher proportions of CHON compounds were observed during PM2.5 events (i.e., days with abnormally high PM2.5 levels) at both sites than on regular or non-event days. </p>
Fig. 4. Particular gomphodesmid structural elements. A. Paxillus – a in A mountain of millipedes IX: Species of the family Gomphodesmidae from the Udzungwa Mountains, Tanzania (Diplopoda, Polydesmida)
Fig. 4. Particular gomphodesmid structural elements. A. Paxillus – a mid-ventral, most often triangular process on body ring 15 in most gomphodesmid males, from Hoffman (2005), modified. B. Torus – a low convexity of variable size and shape, found on the ventral surface of the poriferous paranota in males of many gomphodesmid species. Not drawn to scale.
Annotation and analysis of the secondary structure elements in the Cytochrome P450 protein family
<p>We collected all currently available structures for proteins in the Cytochrome P450 family and annotated their secondary structure elements using SecStrAnnotator software (https://webchem.ncbr.muni.cz/Wiki/SecStrAnnotator). We used 2nnjA as the template domain for the annotation. Based on these annotations, we analysed the occurrence, length distribution, amino acid sequence, and presence of structural irregularities (β-bulges, 3<sub>10</sub>-helices, π-helices) of each secondary structure element class. We also statistically compared the bacterial vs eukaryotic structures. For the secondary structure element classes with sufficient sequence conservation, the most conserved residue is annotated as the reference residue.</p> <p>Main files:</p> <ul> <li><strong>set_ALL.json</strong> - Set-ALL: list of 1012 protein domains belonging to the Cytochrome P450 family (CATH accession 1.10.630.10 + Pfam accession PF00067, accessed on 7 July 2020, one domain per PDB entry)</li> <li><strong>set_NR.json</strong> - Set-NR: non-redundant list of 183 domains (one domain per UniProt ID)</li> <li><strong>domain_lists_table.tsv</strong> - Overview of Set-ALL and Set-NR and separation into subsets Set-NR-Bact (bacterial), Set-NR-Euka (eukaryotic), Set-NR-Arch (archaeal), Set-NR-Viru (viral)</li> <li><strong>structures/template_2NNJ-template.sses.json</strong> - Manually prepared annotation template (domain 2nnjA)</li> <li><strong>structures/template_2NNJ.cif</strong> - Structure of the template domain (2nnjA)</li> <li><strong>annotations_with_reference_residues_ALL.json, annotations_with_reference_residues_ALL.tsv</strong> - Annotation of secondary structure elements for Set-ALL</li> <li><strong>annotations_with_reference_residues_NR.json, annotations_with_reference_residues_NR.tsv</strong> - Annotation of secondary structure elements for Set-NR</li> <li><strong>aligments_NR</strong> - Multiple sequence alignments for each SSE class (Set-NR)</li> <li><strong>logos_NR</strong> - Sequence logos for each SSE class (Set-NR)</li> <li><strong>plots</strong> - Plots of SSE occurrence, length distribution, contained helix types and beta-bulge occurrence (Set-NR), some plots show the comparison between Set-NR-Bact and Set-NR-Euka</li> <li><strong>statistical_tests.ods</strong> - Comparison of SSE occurrence between Set-NR-Bact and Set-NR-Euka by the test of equal proportions and the Fisher test, comparision of the SSE length by the Kolmogorov-Smirnov test and the two-sample Wilcoxon test</li> </ul>
Data from: Primers to highly conserved elements optimized for qPCR-based telomere length measurements in vertebrates
<p>Telomere length dynamics are an established biomarker of health and aging in animals. The study of telomeres in numerous species has been facilitated by methods to measure telomere length by real-time quantitative PCR (qPCR). In this method, telomere length is determined by quantifying the amount of telomeric DNA repeats in a sample and normalizing this to the total amount of genomic DNA. This normalization requires the development of genomic reference primers suitable for qPCR, which remains challenging in non-model organism with genomes that have not been sequenced. Here we report reference primers that can be used in qPCR to measure telomere lengths in any vertebrate species. We designed primer pairs to amplify genetic elements that are highly conserved between evolutionarily distant taxa and tested them in species that span the vertebrate tree of life. We report five primer pairs that meet the specificity and reproducibility standards of qPCR. In addition, we demonstrate an approach to choose the best primers for a given species by testing the primers on multiple individuals within a species and then applying an established computational tool. These reference primers can facilitate qPCR-based telomere length measurements in any vertebrate species of ecological or economic interest.</p>
Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations
The interactions between transposable elements (TEs) and their hosts constitute one of the most profound co-evolutionary processes found in nature. The population dynamics of TEs depends on factors specific to each TE families, such as the rate of transposition and insertional preference, the demographic history of the host and the genomic landscape. How these factors interact has yet to be investigated holistically. Here we are addressing this question in the green anole ( Anolis carolinensis ) whose genome contains an extraordinary diversity of TEs (including non-LTR retrotransposons, SINEs, LTR-retrotransposons and DNA transposons). We observe a positive correlation between recombination rate and TEs frequencies and densities for LINEs, SINEs and DNA transposons. For these elements, there was a clear impact of demography on TE frequency and abundance, with a loss of polymorphic elements and skewed frequency spectra in recently expanded populations. On the other hand, some LTR-retrotransposons displayed patterns consistent with a very recent phase of intense amplification. To determine how demography, genomic features and intrinsic properties of TEs interact we ran simulations using SLiM3. We determined that i) short TE insertions are not strongly counter-selected, but long ones are, ii) neutral demographic processes, linked selection and preferential insertion may explain positive correlations between average TE frequency and recombination, iii) TE insertions are unlikely to have been massively recruited in recent adaptation. We demonstrate that deterministic and stochastic processes have different effects on categories of TEs and that a combination of empirical analyses and simulations can disentangle these mechanisms.
Automated X-ray computer tomography segmentation method for finite element analysis of non-crimp fabrics reinforced composites
<p>Data behind the publications:</p> <p>Auenhammer, R.M., Mikkelsen, L.P., Asp, L., Blinzler, B. Automated X-ray computer tomography segmentation method for finite element analysis of non-crimp fabric reinforced composites. <em>Composite Structures, </em><strong>256</strong>, 113136, <a href="https://doi.org/10.1016/j.compstruct.2020.113136">https://doi.org/10.1016/j.compstruct.2020.113136</a>, 2021.</p> <p>Auenhammer, Robert M., Lars P. Mikkelsen, Leif E. Asp, Brina J. Blinzler, Dataset of non-crimp fabric reinforced composites for an X-ray computer tomography aided engineering process, <em>Data in Brief, </em><strong>33</strong>, 106518, <a href="https://doi.org/10.1016/j.dib.2020.106518">https://doi.org/10.1016/j.dib.2020.106518</a>, 2020.</p> <p>Auenhammer, R.M., L.P. Mikkelsen, L.E. Asp, B.J. Blinzler, X-ray tomography based numerical analysis of stress concentrations in non-crimp fabric reinforced composites - assessment of segmentation methods. <em>IOP Conf. Ser.: Mater. Sci. Eng.</em> <strong>942</strong>, 012038, <a href="https://doi.org/10.1088/1757-899X/942/1/012038">https://doi.org/10.1088/1757-899X/942/1/012038</a>, 2020</p> <p>The data-set contain data from three samples: A, E and G. </p> <p>For each sample the data are saved in the follow format</p> <ul> <li>X-ray scan: nii-files</li> <li>SEM scan: tif-files</li> <li>Abaqus files: inp-files </li> <li>X-ray setting: pdf-files</li> <li>SEM settings: hdr-ascii files</li> </ul> <p> </p>
Stability of elemental content correlates with plant resistance to soil impoverishment
<p><i>Aims</i> We investigated whether plant resistance to soil impoverishment would depend on their flexibility in taking up nutrients and on maintaining elemental stoichiometry.</p> <p><i>Methods</i> We mixed sand with grassland soil in mass proportions of 0, 10, 30, 50 and 70% to simulate soil impoverishment as caused by a gradient of desertification intensity and examined how plant nitrogen (N) uptake (<sup>15</sup>NH<sub>4</sub>NO<sub>3</sub> and NH<sub>4</sub><sup>15</sup>NO<sub>3</sub> labelling) and nutrient stoichiometry were associated with plant growth responses of a sedge (<i>Carex duriuscula</i>) and a forb (<i>Potentilla chinensis</i>).</p> <p><i>Results</i> With increasing intensity of soil impoverishment, plant biomass, cover and density decreased for <i>C. duriuscula</i>, but not for <i>P. chinensis</i>. Interestingly, uptake of both <sup>15</sup>NO<sub>3</sub><sup>-</sup> and <sup>15</sup>NH<sub>4</sub><sup>+</sup> increased for the sedge but not for the forb, with the former species showing stronger preference of NO<sub>3</sub><sup>-</sup>. However, the sedge showed decreasing nutrient contents and concentrations of phosphorus (P) and magnesium (Mg), and thus increasing stoichiometric ratios of N:P and calcium (Ca):Mg. In contrast,<i> </i>the forb maintained its biomass by showing strong stability in nutrient content, concentration and stoichiometry.</p> <p><i>Conclusions</i> Stability of N uptake and nutrient stoichiometry were associated with higher resistance to soil impoverishment of<i> </i>the forb<i> </i>than the sedge. Our study highlights the importance of stability in nutrient uptake and stoichiometry for determining plant-species resistance to nutrient-poor conditions.</p>
Adjudicating national context – elements of legal pluralism in the practice(s) of the European Court of Human Rights?
<p>Dataset for submission til German Law Journal. See Readme.txt for details.</p>
Data from: Model sensitivity and use of the comparative finite element method in mammalian jaw mechanics: mandible performance in the Gray Wolf
Finite Element Analysis (FEA) is a powerful tool gaining use in studies of biological form and function. This method is particularly conducive to studies of extinct and fossilized organisms, as models can be assigned properties that approximate living tissues. In disciplines where model validation is difficult or impossible, the choice of model parameters and their effects on the results become increasingly important, especially in comparing outputs to infer function. To evaluate the extent to which performance measures are affected by initial model input, we tested the sensitivity of bite force, strain energy, and stress to changes in seven parameters that are required in testing craniodental function with FEA. Simulations were performed on FE models of a Gray Wolf (Canis lupus) mandible. Results showed that unilateral bite force outputs are least affected by the relative ratios of the balancing and working muscles, but only ratios above 0.5 provided balancing-working side joint reaction force relationships that are consistent with experimental data. The constraints modeled at the bite point had the greatest effect on bite force output, but the most appropriate constraint may depend on the study question. Strain energy is least affected by variation in bite point constraint, but larger variations in strain energy values are observed in models with different number of tetrahedral elements, masticatory muscle ratios and muscle subgroups present, and number of material properties. These findings indicate that performance measures are differentially affected by variation in initial model parameters. In the absence of validated input values, FE models can nevertheless provide robust comparisons if these parameters are standardized within a given study to minimize variation that arise during the model-building process. Sensitivity tests incorporated into the study design not only aid in the interpretation of simulation results, but can also provide additional insights on form and function.
Data from: Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation
Variation in the presence or absence of transposable elements (TEs) is a major source of genetic variation between individuals. Here, we identified 23,095 TE presence/absence variants between 216 Arabidopsis accessions. Most TE variants were rare, and we find these rare variants associated with local extremes of gene expression and DNA methylation levels within the population. Of the common alleles identified, two thirds were not in linkage disequilibrium with nearby SNPs, implicating these variants as a source of novel genetic diversity. Many common TE variants were associated with significantly altered expression of nearby genes, and a major fraction of inter-accession DNA methylation differences were associated with nearby TE insertions. Overall, this demonstrates that TE variants are a rich source of genetic diversity that likely plays an important role in facilitating epigenomic and transcriptional differences between individuals, and indicates a strong genetic basis for epigenetic variation.
Data from: A selfish genetic element linked to increased lifespan impacts metabolism in female house mice
Gene drive systems can lead to the evolution of traits that further enhance the transmission of the driving element. In gene drive, one allele is transmitted to offspring at a higher frequency than the homologous allele. This has a range of consequences, which generally include a reduction in fitness of the carrier of the driving allele, making such systems <i>selfish</i>. The t haplotype is one such driver, found in house mice. It is linked to a reduction in litter size in matings among heterozygous animals, but also to increased lifespan in wild females that carry it. Here, we tested whether carrying the t haplotype was associated with altered resting metabolic rate (RMR). We show that females carrying the t haplotype decrease RMR as they increase in size, compared to wildtype females or males of either genotype. Our study elucidates a plausible mechanism by which a selfish genetic element increases lifespan.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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