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145 results for “structure formation”
Microbial Observatory at North Temperate Lakes LTER High-resolution temporal and spatial dynamics of microbial community structure in freshwater bog lakes 2005 - 2009 original format (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-ntl/349/4. The abstract below was extracted from the Level 0 data package and is included for context: The North Temperate Lakes - Microbial Observatory seeks to study freshwater microbes over long time scales (10+ years). Observing microbial communities over multiple years using DNA sequencing allows in-depth assessment of diversity, variability, gene content, and seasonal/annual drivers of community composition. Combining information obtained from DNA sequencing with additional experiments, such as investigating the biochemical properties of specific compounds, gene expression, or nutrient concentrations, provides insight into the functions of microbial taxa. Our 16S rRNA gene amplicon datasets were collected from bog lakes in Vilas County, WI, and from Lake Mendota in Madison, WI. Ribosomal RNA gene amplicon sequencing of freshwater environmental DNA was performed on samples from Crystal Bog, North Sparkling Bog, West Sparkling Bog, Trout Bog, South Sparkling Bog, Hell’s Kitchen, and Mary Lake. These microbial time series are valuable both for microbial ecologists seeking to understand the properties of microbial communities and for ecologists seeking to better understand how microbes contribute to ecosystem functioning in freshwater.
Microbial Observatory at North Temperate Lakes LTER High-resolution temporal and spatial dynamics of microbial community structure in freshwater bog lakes 2005 - 2009 original format
The North Temperate Lakes - Microbial Observatory seeks to study freshwater microbes over long time scales (10+ years). Observing microbial communities over multiple years using DNA sequencing allows in-depth assessment of diversity, variability, gene content, and seasonal/annual drivers of community composition. Combining information obtained from DNA sequencing with additional experiments, such as investigating the biochemical properties of specific compounds, gene expression, or nutrient concentrations, provides insight into the functions of microbial taxa. Our 16S rRNA gene amplicon datasets were collected from bog lakes in Vilas County, WI, and from Lake Mendota in Madison, WI. Ribosomal RNA gene amplicon sequencing of freshwater environmental DNA was performed on samples from Crystal Bog, North Sparkling Bog, West Sparkling Bog, Trout Bog, South Sparkling Bog, Hell’s Kitchen, and Mary Lake. These microbial time series are valuable both for microbial ecologists seeking to understand the properties of microbial communities and for ecologists seeking to better understand how microbes contribute to ecosystem functioning in freshwater.
cldf-datasets/szetosinitic: Chinese Structure Dataset from Szeto et al.'s (2018) paper in CLDF-Format
<p>This is a structural dataset originally published along with a paper by Szeto et al. (2018) on Chinese dialect classification:</p> <blockquote> <p>Szeto, P. Y.; Ansaldo, U. & Matthews, S.Typological variation across Mandarin dialects: An areal perspective with a quantitative approach Linguistic Typology, 2018, 22, 233-275.</p> </blockquote>
LIPID MAPS® Structure Database (LMSD) formatted for MetFrag
<p>This repository contains the LIPID MAPS® Structure Database (<a href="https://www.lipidmaps.org/databases/lmsd/overview">LMSD</a>) formatted for use in <a href="https://msbi.ipb-halle.de/MetFrag/">MetFrag</a> (and other workflows).</p> <p><em>LIPID MAPS® Lipidomics Gateway is a free, comprehensive website for researchers interested in lipid biology. Use <a href="https://www.lipidmaps.org"> https://www.lipidmaps.org</a> to stay abreast of developments each month from across the field, and explore the rich information collections, tools and resources from the LIPID Metabolites And Pathways Strategy (LIPID MAPS®) Consortium. </em><br> </p> <p>The workflow used to create this file (by B. Talavera Andújar) can be found here: <a href="https://gitlab.lcsb.uni.lu/eci/simple-utilities/sdf2csv">https://gitlab.lcsb.uni.lu/eci/simple-utilities/sdf2csv</a></p> <p><strong>Reference:</strong> LMSD: LIPID MAPS® structure database, Sud M., Fahy E., Cotter D., Brown A., Dennis E., Glass C., Murphy R., Raetz C., Russell D., and Subramaniam S., Nucleic Acids Research, 2006, DOI: <a href="https://doi.org/10.1093/nar/gkl838"> 10.1093/nar/gkl838 </a></p>
Microbial Observatory at North Temperate Lakes LTER High-resolution temporal and spatial dynamics of microbial community structure in freshwater bog lakes 2005 - 2009 original format (Reformatted to a Darwin Core Archive)
This data package is formatted as a Darwin Core Archive (DwC-A, event core). For more information on Darwin Core see https://www.tdwg.org/standards/dwc/. This Level 2 data package was derived from the Level 1 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-ntl/344/6, which was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-ntl/349/4. The abstract below was extracted from the Level 0 data package and is included for context: The North Temperate Lakes - Microbial Observatory seeks to study freshwater microbes over long time scales (10+ years). Observing microbial communities over multiple years using DNA sequencing allows in-depth assessment of diversity, variability, gene content, and seasonal/annual drivers of community composition. Combining information obtained from DNA sequencing with additional experiments, such as investigating the biochemical properties of specific compounds, gene expression, or nutrient concentrations, provides insight into the functions of microbial taxa. Our 16S rRNA gene amplicon datasets were collected from bog lakes in Vilas County, WI, and from Lake Mendota in Madison, WI. Ribosomal RNA gene amplicon sequencing of freshwater environmental DNA was performed on samples from Crystal Bog, North Sparkling Bog, West Sparkling Bog, Trout Bog, South Sparkling Bog, Hell’s Kitchen, and Mary Lake. These microbial time series are valuable both for microbial ecologists seeking to understand the properties of microbial communities and for ecologists seeking to better understand how microbes contribute to ecosystem functioning in freshwater.
Tabular datasets for "In situ structural analysis reveals membrane shape transitions during autophagosome formation"
<p>Tabular source data for all plots in the manuscript "In situ structural analysis reveals membrane shape transitions during autophagosome formation". The article is available at https://doi.org/10.1101/2022.05.02.490291. The naming of the sheets in the .xlsx files corresponds to the figure number and panel.</p>
Observation of a regular structure formation on the surface of vibrated ball beds started from random lose packing
<p>Near 4,000 2-mm diameter plastic balls were poured 88 times into plexiglass cylinder of internal diameter 26 mm. Then, such initially random loose-packing systems/beds were vibrated vertically with 100 Hz frequency using the vibration table Vibrax (Renfert GmbH, Germany) working in sinusoidal mode until a regular structure was observed on the cylinder surface. The power levels of the vibrations in the recorded ordering of balls were selected to represent all four levels (1, 2, 3 or 4) of vibrations available in the table, where number 1 means the weakest vibration and 4 means the strongest one.</p> <p>Locations of the balls on all sides of a vibrated cylindrical bed were simultaneously recorded on one video frame thanks to the use of two perpendicular mirrors, which enables observation of four images: one of the real cylinder and three of its mirror reflections. View of the table with the attached cylinder containing balls and two mirrors is presented in Fig. 1, while an explanation of the scene, as seen by the recording camera, is given in the scheme in Fig. 2. Video names were given in a standard form explained in the README.txt file.</p>
Movement of plastic balls in a long-vibrating cylinder: from disorder to structure formation with examples of its instability
<p>Many plastic balls, made from PolyOxyMethylene (POM) and of three different diameters 2, 3 and 4 mm, were used to observe the formation and stability of the structure in ball beds when, after pouring into a plexiglass cylinder, they were subjected to long-term vertical vibrations with frequency 100 Hz. The vibration table Vibrax (Renfert GmbH, Germany), used in the experiment and shown in Fig. 1, can function in two modes: sinusoidal (s) and nonsinusoidal (ns). The vibration table can act at four power levels of the vibrations, selected by an operator using the right knob of the table (see Fig. 1). In the presented series of 43 vibration experiments, always the highest power level was used. </p> <p>Locations of surface balls on all sides of a vibrated cylindrical bed were simultaneously recorded on one video frame thanks to the use of two perpendicular mirrors (see Fig. 1), which enables observation of four images: one of the real cylinder and three of its mirror reflections. An explanation of the scene, as seen by the recording camera, is given in the scheme in Fig. 2. Video names were given in a standard form to inform the user about the most important parameters (more in README.txt).</p> <p> </p>
Dataset for article: Structure Formation in Tailor-Made Buriti Oil Emulsion During Simulated Digestion
<p><strong>Dataset for publication:</strong></p> <p>Structure Formation in Tailor-Made Buriti Oil Emulsion During Simulated Digestion<br> <em>Rafael V. M. Freire, Linda Hong, Miroslav Peterek, Stéphane Canarelli, Serge Rezzi, Stefan Salentinig</em><br> Advanced Funtional Materials 2023 (DOI 10.1002/adfm.202303854)</p> <p>Setup and conditions for the experiments are described in the experimental section of the published (open access) manuscript.</p> <p>Data description in README.txt file.</p>
SI data: A high-throughput structural and electrochemical study of metallic glass formation in Ni-Ti-Al
<p>Journal: ACS Combinatorial Science<br> Title: A high-throughput structural and electrochemical study of metallic glass formation in Ni-Ti-Al<br> Author(s): Joress, Howie; DeCost, Brian; sarker, suchismita; Braun, Trevor; Jilani, Sidra; Smith, Ryan; Ward, Logan; Laws, Kevin; Mehta, Apurva; Hattrick-Simpers, Jason</p>
Protein secondary-structure description with a coarse-grained model: code and datasets in ActivePapers format
<p>This file contains the supplementary material for the publication</p> <p><em>Protein secondary-structure description with a coarse-grained model</em><br /> by Gerald R. Kneller and K. Hinsen<br /> http://dx.doi.org/10.1107/S1399004715007191<br /> Acta Cryst. (2015). D<strong>71</strong>, 1411-1422</p> <p><strong>Datasets in this file</strong></p> <p>1) ScrewFit and ScrewFrame parameters for ideal secondary-structure elements</p> <p> Scripts:<br /> /code/import_ideal_structures<br /> /code/analyze_ideal_structures</p> <p>1.1) The PDB files generated with Chimera</p> <p> /data/ideal_structures/3-10.pdb<br /> /data/ideal_structures/alpha.pdb<br /> /data/ideal_structures/beta-antiparallel.pdb<br /> /data/ideal_structures/beta-parallel.pdb<br /> /data/ideal_structures/pi.pdb</p> <p>1.2) The corresponding MOSAIC datasets</p> <p> /data/ideal_structures/3-10<br /> /data/ideal_structures/alpha<br /> /data/ideal_structures/beta-antiparallel<br /> /data/ideal_structures/beta-parallel<br /> /data/ideal_structures/pi</p> <p>1.3) The ScrewFit parameters</p> <p> /data/ideal_structures/screwfit/3-10<br /> /data/ideal_structures/screwfit/alpha<br /> /data/ideal_structures/screwfit/beta-antiparallel<br /> /data/ideal_structures/screwfit/beta-parallel<br /> /data/ideal_structures/screwfit/pi</p> <p>1.4) The ScrewFrame parameters</p> <p> /data/ideal_structures/screwframe/3-10<br /> /data/ideal_structures/screwframe/alpha<br /> /data/ideal_structures/screwframe/beta-antiparallel<br /> /data/ideal_structures/screwframe/beta-parallel<br /> /data/ideal_structures/screwframe/pi</p> <p><br /> 2) Statistics for ScrewFit and ScrewFrame parameters computed<br /> for the ASTRAL SCOPe subset with less than 40% sequence identity.</p> <p> Scripts:<br /> /code/astral_analysis<br /> /code/fit_rho_distributions<br /> /code/plot_histograms</p> <p>2.1) The ASTRAL database (link to published ActivePaper)</p> <p> /data/astral_2.04</p> <p>2.2) The histograms for the ScrewFit and ScrewFrame parameters<br /> for the all-alpha and all-beta subsets</p> <p> /data/histograms/astral_alpha/screwfit<br /> /data/histograms/astral_alpha/screwframe</p> <p> /data/histograms/astral_beta/screwfit<br /> /data/histograms/astral_beta/screwframe</p> <p>2.3) The Gaussians fitted to the peaks in the distributions for rho</p> <p> /data/fitted_rho_distributions/screwfit<br /> /data/fitted_rho_distributions/screwframe</p> <p>2.4) Plots</p> <p> /documentation/delta.pdf<br /> /documentation/delta_q.pdf<br /> /documentation/delta_r.pdf<br /> /documentation/p.pdf<br /> /documentation/rho-detail.pdf<br /> /documentation/rho.pdf<br /> /documentation/sigma.pdf<br /> /documentation/tau.pdf</p> <p><br /> 3) Comparison of secondary-structure identification between ScrewFrame<br /> and DSSP.</p> <p> Script:<br /> /code/compare_secondary_structure_assignments<br /> /code/plot_histograms</p> <p>3.1) The histograms of the lengths of secondary-structure elements</p> <p> /data/histograms/secondary_structure/length-alpha-dssp<br /> /data/histograms/secondary_structure/length-alpha-screwframe<br /> /data/histograms/secondary_structure/length-beta-dssp<br /> /data/histograms/secondary_structure/length-beta-screwframe</p> <p>3.2) The 2D histograms of the number of residues inside identified<br /> secondary-structure elements</p> <p> /data/histograms/secondary_structure/n-alpha<br /> /data/histograms/secondary_structure/n-beta</p> <p>3.3) The distribution of rho inside alpha helices</p> <p> /data/histograms/secondary_structure/rho-alpha-dssp</p> <p>3.3) Plots</p> <p> /documentation/lengths-alpha.pdf<br /> /documentation/lengths-beta.pdf<br /> /documentation/n-alpha.pdf<br /> /documentation/n-beta.pdf<br /> /documentation/rho-alpha-dssp.pdf</p> <p><br /> 4) Illustration for myoglobin and VADC-1</p> <p> Scripts:<br /> /code/import_myoglobin_vdac<br /> /code/analyze_myoglobin<br /> /code/analyze_vdac<br /> /code/perturbation_analysis</p> <p>4.1) Imported structures in MOSAIC format:<br /> PDB code 1A6G for myoglobin<br /> PDB code 2K4T for VDAC-1</p> <p> /data/myoglobin<br /> /data/VDAC-1</p> <p>4.2) Plots showing rho and delta</p> <p> /documentation/rho-myoglobin.pdf<br /> /documentation/delta-myoglobin.pdf</p> <p>4.3) Tube models for visualization with Chimera</p> <p> /documentation/myoglobin-tube.bld<br /> /documentation/VDAC-1-tube.bld</p> <p>4.4) Sensitivity to perturbations in the coordinates</p> <p> /documentation/rho-perturbed-myoglobin.pdf<br /> /documentation/delta-perturbed-VDAC-1.pdf<br /> /documentation/rho-perturbed-myoglobin.pdf<br /> /documentation/delta-perturbed-VDAC-1.pdf<br /> /documentation/myoglobin-perturbation.pdf<br /> /documentation/VDAC-1-perturbation.pdf</p> <p>5) Analysis of CA-only structures in the PDB</p> <p> Scripts:<br /> /code/ca_analysis<br /> /code/import_calpha_structures<br /> /code/plot_histograms</p> <p>5.1) Imported CA-only structures in MOSAIC format</p> <p> /data/pdb_ca_only_structures</p> <p>5.2) Histograms for ScrewFrame parameters</p> <p> /data/histograms/ca_only_structures</p> <p>5.3) Plots</p> <p> /documentation/delta_ca.pdf<br /> /documentation/delta_q_ca.pdf<br /> /documentation/delta_r_ca.pdf<br /> /documentation/p_ca.pdf<br /> /documentation/rho_ca.pdf<br /> /documentation/sigma_ca.pdf<br /> /documentation/tau_ca.pdf</p> <p> </p>
(U)SAXS data (ID02 beamline, ESRF): Effects of pH on the fibrous structure formation of plant proteins during high-moisture extrusion
<p>Due to health and environmental factors, the food industry is looking for ways to introduce meat replacers made from plant-based proteins to consumer markets. The presence of structural anisotropy in the form of fibre is a prerequisite for meat analogues. Structure formation ability depends on the protein ingredients used, which leads to plant protein products with varying texture hardness and extent of fibre alignment. In the current study, we will test if it is possible to tune these properties based on the hypothesis that plant proteins have different structure formation abilities under varying pH conditions.</p>
Raw data for: A model for the formation and evolution of structure of initial loess deposits
<p>The dataset includes the monitoring results of volumetric water content and matric suction during wetting and drying processes of initial loess deposits. The data are used for Figure 3 in the manuscript “A model for the formation and evolution of structure of initial loess deposits” (submitted to Geophysical Research Letters).</p>
Dataset for Effect of matrix solidification on the structure formation in electromagnetic suspensions
<p><strong>Introduction:</strong> Dataset from numerical simulations describing the structure formation in suspensions with electromagnetically active particles in an external field, as described in detail in the paper</p> <ul> <li>Konstantinos Manikas, Markus Hütter, Patrick D. Anderson: Effect of matrix solidification on the structure formation in electromagnetic suspensions. Appl. Phys. A, 128: 709 (11 pages), 2022. DOI: 10.1007/s00339-022-05844-y WWW: https://doi.org/10.1007/s00339-022-05844-y</li> </ul> <p>which should be cited whenever this dataset is used. The data compiled here is the basis for figures 4, 5, and 6 in that paper.</p> <p> </p> <p><strong>Format:</strong> The files are provided in plain-text format (ascii).</p> <p> </p> <p><strong>Filenames:</strong> The nomenclature for the filenames follows the following scheme:</p> <ul> <li>data_fig{number}_{param}_{value}.txt</li> </ul> <p>where {number} specifies the number of the figure in the paper, {param} is the parameter that is studied and {value} denotes its numerical value (see the paper for details).</p> <p> </p> <p><strong>File content:</strong> Each datafile contains 1 header line, in which the meaning of the data-columns are explained (time, S2, N*, lambda* -- see paper for details), and the studied parameter and its value are listed. After this header line, the data is presented in tab-delimited columns.</p> <p> </p> <p>For further details, the reader is referred to the paper mentioned above.</p>
Structure of MAPbI3 surface models in VASP format
<p>Structure of MAPbI<sub>3</sub> surface models in VASP format, with the slab thickness of 6 stoichiometric units, along (001) planes. These models were generated for the study published in reference 1.</p> <p>(1) Lodeiro, L.; Barría-Cáceres, F.; Jiménez, K.; Contreras, R.; Montero-Alejo, A. L.; Menéndez-Proupin, E. Methodological Issues in First-Principle Calculations of CH3NH3PbI3 Perovskite Surfaces: Quantum Confinement and Thermal Motion. <em>ACS Omega</em> <strong>2020</strong>, <em>5</em> (45), 29477–29491. https://doi.org/10.1021/acsomega.0c04420.</p>
Microfluidic solvent extraction of poly(vinyl alcohol) droplets: effect of polymer structure on particle and capsule formation
<p>Raw data from the majority of figures of our 2018 Soft Matter Paper:</p> <p>Selected datasets from figures are excluded, owing to them being transformations of the raw data provided in the same figure.</p> <p> </p>
Fig. 9 in Form and formation of flares and parabolae based on new observations of the internal shell structure in lytoceratid and perisphinctid ammonoids
Fig. 9. Transition of parabolae and flares in Analytoceras hermanni (Gümbel, 1868) (BSPG Man-x) from Bihati river valley south of Baun, SW Timor, Hettangian, Jurassic (compare Hoffmann and Keupp 2010); in ventral (A) and lateral (B) views.
Fig. 8 in Form and formation of flares and parabolae based on new observations of the internal shell structure in lytoceratid and perisphinctid ammonoids
Fig. 8. Internal structure of parabolae (transversal section) in Choffatia sp. (BSPG MAn-4519) from Dubki near Saratov, SW Russia; Upper Callovian, Jurassic. A. Parabola with notches. B–E. Discontinuity of the parabolae, the primary shell forms slots at the position of the notches. A secondary shell is attached from beneath. The relief is compensated by the dorsal inner prismatic layer. Abbreviations: apc, apertural prismatic coating; dipl, dorsal inner prismatic layer; ipl, inner prismatic layer; ncl 1/2, nacreous layer of the primary/secondary shell.
Fig. 7 in Form and formation of flares and parabolae based on new observations of the internal shell structure in lytoceratid and perisphinctid ammonoids
Fig. 7. Internal structure of parabolae (median section, growth direction right) in Choffatia sp. (BSPG MAn-4520) from Dubki near Saratov, SW Russia; Upper Callovian, Jurassic. A, B. Discontinuity of the parabola, the primary nacreous layer ends abruptly. A secondary nacreous layer is attached from beneath. The relief is compensated by the dorsal inner prismatic layer. C. Discontinuity of parabolae at the position of the notches. The primary shell bends outwards and has an apertural prismatic coating. The secondary shell is attached from beneath. In front of the free edge of the primary shell a symmetric, prismatic thickening is formed. The dorsal shell compensates the relief. D. Lateral parts of the notches show the typical outward undulation of the new shell of the parabolic node. Abbreviations: apc, apertural prismatic coating; dipl, dorsal inner prismatic layer; dncl, dorsal nacreous layer; dopl, dorsal outer prismatic layer; ncl 1/2, nacreous layer of the primary/secondary shell; opl 1/2, outer prismatic layer of the primary/secondary shell; pt, prismatic thickening; S, septum.
Fig. 6 in Form and formation of flares and parabolae based on new observations of the internal shell structure in lytoceratid and perisphinctid ammonoids
Fig. 6. Internal structure of a secondary flare (median section, growth direction right) in Argonauticeras besairiei Collignon, 1949 (BSPG MAo- 1802) from Ambatolafia, Mahajanga Basin, NW Madagascar; Lower Albian, Cretaceous. Abbreviations: apc, apertural prismatic coating; dipl, dorsal inner prismatic layer; ipl, inner prismatic layer; ncl 1/2, nacreous layer of the primary/secondary shell; opl 1/2, outer prismatic layer of the primary/secondary shell; sb, shell bulge.
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