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4,489 results for “transitivity”
Figure 5 from: Baković N, Matoničkin Kepčija R, Siemensma FJ (2022) Transitional and small aquatic cave habitats diversification based on protist assemblages in the Veternica cave (Medvednica Mt., Croatia). Subterranean Biology 42: 43-60. https://doi.org/10.3897/subtbiol.42.78037
Figure 5 Taxon richness and abundance of protist taxa at the sites investigated.
Figure 1 from: Baković N, Matoničkin Kepčija R, Siemensma FJ (2022) Transitional and small aquatic cave habitats diversification based on protist assemblages in the Veternica cave (Medvednica Mt., Croatia). Subterranean Biology 42: 43-60. https://doi.org/10.3897/subtbiol.42.78037
Figure 1 Location of the Veternica cave.
Figure 6 from: Baković N, Matoničkin Kepčija R, Siemensma FJ (2022) Transitional and small aquatic cave habitats diversification based on protist assemblages in the Veternica cave (Medvednica Mt., Croatia). Subterranean Biology 42: 43-60. https://doi.org/10.3897/subtbiol.42.78037
Figure 6 nMDS based on Bray Curtis similarity between samples.
Droplet collapse during strongly supercooled transitions: Movies of collapsing droplets
<p>Movies of collapse of spherically symmetric droplets in a first order phase transition. The movies are based on Figures 5 and 6 of the paper <a href="https://doi.org/10.1103/PhysRevD.106.103524">Droplet collapse during strongly supercooled transitions</a> [<a href="https://arxiv.org/abs/2204.03396">arXiv:2204.03396</a>]. Each movie shows the evolution of the order parameter <span class="math-tex">\(\phi\)</span> relative to the true vacuum value <span class="math-tex">\(\phi_b\)</span>, the fluid velocity <span class="math-tex">\(v\)</span>, and the temperature <span class="math-tex">\(T\)</span> relative to the critcal temperature <span class="math-tex">\(T_c\)</span>. The transition strength, <span class="math-tex">\(\alpha\)</span>, is given in the filename.<br> <br> The movies which include "limits" in the filename have fixed y-axis limits, whereas the other two movies let the y-axis range freely in each frame.</p>
Replication package for: Culture and the Historical Fertility Transition
<p>This package provides the replication files for Beach, Brian and Hanlon, W. Walker (Forthcoming). "Culture and the Historical Fertility Transition", Review of Economic Studies. The replication package includes a README, data, and processing files to create the results presented in the manuscript and the online appendix.</p>
Data from: Gradual assembly of avian body plan culminated in rapid rates of evolution across dinosaur-bird transition
[No abstract entered]
Coordination between metabolic transitions and gene expression by NAD + availability during adipogenic differentiation in human cells
<p>Adipocytes are the main cell type in adipose tissue, a critical regulator of metabolism highly specialized in storing energy as fat. Adipocytes differentiate from multipotent mesenchymal stromal cells through adipogenesis, a tightly controlled differentiation process involving closely interplay between metabolic transitions and sequential programs of gene expression. However, the specific gears driving this interplay remain largely obscure. Additionally, the metabolite nicotinamide adenine dinucleotide (NAD ⁺ ) is becoming increasingly recognized as a regulator of lipid metabolism, is postulated as a promising therapeutic target for dyslipidemia and obesity. Here, we explored the effect of manipulating NAD ⁺ bioavailability during adipogenic differentiation from human mesenchymal stem cells. We found a previously unappreciated strong repressive role for NAD ⁺ on adipocyte commitment, while a functional NAD+-dependent deacetylase SIRT1 appeared crucial for terminal differentiation of pre-adipocytes. Remarkably, repressing the NAD ⁺ biosynthetic salvage pathway during adipogenesis promoted the adipogenic transcriptional program, suggesting that SIRT1 activity during adipogenesis is independent of the NAD ⁺ salvage pathway, while two-photon microscopy and extracellular flux analyses suggest that its activation relies on the metabolic switch. Interestingly, SIRT1-directed control of subcellular compartmentalization of redox metabolism during adipogenesis was evidenced by two-photon fluorescence lifetime microscopy. Significance Statement Adipocyte differentiation occurs from mesenchymal stem cells through the adipogenic process, involving sequential activation of both transcriptional and metabolic programs in a tightly coordinated manner. However, how transcriptional and metabolic transitions reciprocally interact during adipogenic differentiation remains largely obscure. Here we describe that the metabolite NAD ⁺ suppresses adipogenesis through rewiring transcription, while a functional NAD-dependent deacetylase SIRT1 is essential for terminal differentiation of pre-adipocytes. Using two-photon fluorescence lifetime microscopy, we created a metabolic map of NADH and lipid content simultaneously in live cells and described a new role for SIRT1 in the control of compartmentalization of redox metabolism during adipogenesis. These findings advance our understanding to improve therapeutical approaches targeting the NAD ⁺ -SIRT1 axis as a treatment for obesity and dyslipemia.</p>
Data from: No early warning signals for stochastic transitions: insights from large deviation theory
[No abstract entered]
Energy Landscape of the Sugar Conformation Controls the Sol-to- Gel Transition in Self-Assembled Bola Glycolipid Hydrogels
<p>Self-assembled fibrillar network (SAFIN) hydrogels and organogels are commonly obtained by a crystallization process into fibers induced by external stimuli like temperature or pH. The gel-to-sol-to-gel transition is generally readily reversible and the change rate of the stimulus determines the fiber homogeneity and eventual elastic properties of the gels. However, recent work shows that in some specific cases, fibrillation occurs for a given molecular conformation and the sol-to-gel transition depends on the relative energetic stability of one conformation over the other, and not on the rate of change of the stimuli. We observe such a phenomenon on a class of bolaform glycolipids, sophorosides, similar to the well-known sophorolipid biosurfactants, but composed of two symmetric sophorose units. A combination of oscillatory rheology, small-angle X-ray scattering (SAXS) cryogenic transmission electron microscopy (cryo-TEM) and <em>in situ</em> rheo-SAXS using synchrotron radiation shows that below 14°C, twisted nanofibers are the thermodynamic phase. Between 14°C and about 33°C, nanofibers coexist with micelles and a strong hydrogel forms, the sol-to-gel transition being readily reversible in this temperature range. However, above the annealing temperature of about 40°C, the micelle morphology becomes kinetically-trapped over hours, even upon cooling, whichever the rate, to 4°C. A combination of solution and solid-state nuclear magnetic resonance (NMR) suggests two different conformations of the 1ˈˈ, 1ˈ and 2ˈ carbon stereocenters of sophorose, precisely at the β(1,2) glycosidic bond, for which several combinations of the dihedral angles are known to provide at least three energetic minima of comparable magnitude and each corresponding to a given sophorose conformation.</p>
LAMMPS input files and analysis for estimating the glass transition temperature using ensemble molecular dynamcs of a selection of epoxy resins using different protocols for computing the density-temperature behaviour.
<p>LAMMPS input files and analysis for estimating the glass transition temperature using ensemble molecular dynamcs of a selection of epoxy resins using different protocols for computing the density-temperature behaviour. </p>
Quantum circuits reproduce the experimental two-dimensional many-body localization transition point
<p>abstract: While many studies point towards the existence of many-body localization (MBL) in one dimension, the fate of higher-dimensional strongly disordered systems is a topic of current debate. The latest experiments as well as several recent numerical studies indicate that such systems behave many-body localized—at least on practically relevant timescales. However, thus far, theoretical approaches have been unable to quantitatively reproduce experimentally measured MBL features—an important requirement to demonstrate their validity. In this Letter, we use fermionic quantum circuits as a variational method to approximate the full set of eigenstates of two-dimensional MBL systems realized in fermionic optical lattice experiments. Using entanglement-based features, we obtain a phase transition point in excellent agreement with the experimentally measured value. Moreover, we calculate the filling-fraction-dependent MBL phase diagram. We argue that our approach best captures the underlying charge-density-wave experiments and compute the mean localization lengths, which can be compared to future experiments.</p> <p>Access will be granted upon reasonable request.</p>
Supplementary Data for Paper "Efficient Modeling of Water Adsorption in MOFs Using Interpolated Transition Matrix Monte Carlo"
<p>This dataset contains data needed to reproduce all calculations and plots published in paper "Efficient Modeling of Water Adsorption in MOFs Using Interpolated Transition Matrix Monte Carlo", B. Mazur, L. Firlej, and B. Kuchta, 2024, ACS Appl. Mater. Interfaces, DOI: 10.1021/acsami.4c02616. </p>
Flow channelling variability in transit times and tortuosity in a fractured rock model with small scale heterogeneity
<p>Description for file "simulation-particle-data-all-cases".</p> <p>First row is header information, as follows: </p> <p>Column 1, label "avf"<br> The variance of fracture aperture fields (m2)</p> <p>Column 2, label "sdx"<br> The correlation length factor of fracture aperture fields (-)</p> <p>Column 3, label "t"<br> Particle transit time (yr)</p> <p>Column 4, label "log_t"<br> Base-10 logarithm of transit time </p> <p>Column 5, label "l"<br> Particle trajectory length (m)</p> <p>Column 6, label "tort"<br> Particle trajectory tortuosity (-)</p>
Receiver Function Image of the Mantle Transition Zone beneath Western China: Fragmented Subduction and Counterflow Upwelling --- Result Dataset
<p><span>The compressed file contains the 3-D mantle transition zone imaging results of western China and its neighboring regions, including the depths of the 410- and 660-km discontinuities and the MTZ thicknesses.</span></p>
Thermoelastic anomaly of iron carbonitride across the spin transition and implications for planetary cores
<p>This is the dataset for the manuscript entitled "Thermoelastic anomaly of iron carbonitride across the spin transition and implications for planetary cores".</p>
Figure 1 in Small mammals and microhabitat selection in forest fragments in the transition zone between Atlantic Forest and Pampa biome
Figure 1. Location of the study area in South America and Rio Grande do Sul State, Brazil. Atlantic Forest and Pampa biome extents in the Rio Grande do Sul. Regional landscape with forest fragments, main roads, and matrix extent. Numbers 1 and 2 indicate the studied fragments (Fragment 1 – 28°08′38″S, 54°45′36″W, 30 ha, Fragment 2 – 28°07′33″S, 54°44′57″W, 20 ha).
Figure 2 in Small mammals and microhabitat selection in forest fragments in the transition zone between Atlantic Forest and Pampa biome
Figure 2. Number of individuals captured for the four most abundant species of small mammals in two forest fragments of Atlantic Forest between Autumn 2015 and Spring 2016 in Cerro Largo, Rio Grande do Sul, Brazil. (A) Akodon montensis; (B) Oligoryzomys nigripes; (C) Sooretamys angouya; (D) Didelphis albiventris. F1 = Fragment 1; F2 = Fragment 2.
Geometries for "Reduced Scaling Correlated Natural Transition Orbitals for Multilevel Coupled Cluster Calculations"
<p>Formaldehyde, formaldehyde-in-water, and azobenzene dye geometries used in "Reduced Scaling Correlated Natural Transition Orbitals for Multilevel Coupled Cluster Calculations" in xyz-format.</p>
Repository for: "Localization-delocalization transition for light particles in turbulence"
<div>This respository contains underlying data and figure scripts, corresponding to the article "Localization-delocalization transition for light particles in turbulence", Z, Wang, X.M. de Wit, F. Toschi, 2024, PNAS</div> <div> </div> <div> </div> <div><strong>Figures and data</strong></div> <div>Scripts to the figures covered in the article are provided in the directory 'Figures_and_data' along with the required data from the Direct Numerical Simulations.</div> <div> </div> <div>Below, we give a list of the files corresponding to each figure.</div> <div> </div> <div><em>Main text</em></div> <ul> <li>Fig. 1: panels a, b, c, and d are plotted by Figures_and_data/FIG1/fig1_a_b_c_d.m; panel f is plotted by Figures_and_data/FIG1/fig1_f.m</li> <li> <div>Fig. 2: panels a, e, g, and i are plotted by Figures_and_data/FIG2/fig2_a_e_g_i.m; panels f, h, and j are plotted by Figures_and_data/FIG2/fig2_f_h_j.m</div> </li> <li> <div>Fig. 3: n/a</div> </li> <li> <div>Fig. 4: panel e is plotted by Figures_and_data/FIG4/fig1_e.m; panels f and g are plotted by Figures_and_data/FIG4/fig4_f_g.ipynb</div> </li> <li> <div>Fig. 5: panels a and c are plotted by Figures_and_data/FIG5/fig5_a_c.ipynb; panels b, d and e are plotted by Figures_and_data/FIG5/fig5_b_d_e.m</div> </li> </ul> <div><em>Supplemental Information</em></div> <div> <ul> <li>Fig. S1: fig.S1 is plotted by Figures_and_data/SUPPLEMENTARY_INFORMATION/figS1.ipynb</li> <li>Fig. S2: panels a, b, and c are plotted by Figures_and_data/SUPPLEMENTARY_INFORMATION/figS2.m; panel d is plotted by Figures_and_data/FIG4/fig4_f_g.ipynb</li> <li>Fig. S3: panels a and b are plotted by Figures_and_data/SUPPLEMENTARY_INFORMATION/figS3_a_b.ipynb; panels c-f are plotted by Figures_and_data/SUPPLEMENTARY_INFORMATION/figS3_c_d_e_f.ipynb</li> <li>Fig. S4: fig, S4 is plotted by Figures_and_data/SUPPLEMENTARY_INFORMATION/figS4.ipynb</li> <li>Fig. S5: fig, S5 is plotted by Figures_and_data/SUPPLEMENTARY_INFORMATION/figS5.ipynb</li> <li>Fig. S6: panel b is plotted by Figures_and_data/FIG4/fig4_f_g.ipynb; all the other panels are plotted by Figures_and_data/SUPPLEMENTARY_INFORMATION/figS6_S7_S8_S10_S11.ipynb</li> <li>Fig. S7: panel b is plotted by Figures_and_data/FIG4/fig4_f_g.ipynb; all the other panels are plotted by Figures_and_data/SUPPLEMENTARY_INFORMATION/figS6_S7_S8_S10_S11.ipynb</li> <li>Fig. S8: panel b is plotted by Figures_and_data/FIG4/fig4_f_g.ipynb; all the other panels are plotted by Figures_and_data/SUPPLEMENTARY_INFORMATION/figS6_S7_S8_S10_S11.ipynb</li> <li>Fig. S9: panels a and b are plotted by Figures_and_data/SUPPLEMENTARY_INFORMATION/figS9.m</li> <li>Fig. S10: panels a,b,c and e,f,g, and i,j,k are plotted by Figures_and_data/SUPPLEMENTARY_INFORMATION/figS6_S7_S8_S10_S11.ipynb; panels d, h, and f are plotted by Figures_and_data/FIG4/fig4_f_g.ipynb</li> <li>Fig. S11: fig, S11 is plotted by Figures_and_data/SUPPLEMENTARY_INFORMATION/figS6_S7_S8_S10_S11.ipynb</li> </ul> <p> </p> </div> <div><strong>Authors</strong></div> <div>Z, Wang, X.M. de Wit, F. Toschi</div> <div> </div> <div> </div> <div><strong>License</strong></div> <div>All code is released under the 2-clause BSD license (see LICENSE).</div>
Graph neural networks for predicting metal–ligand coordination of transition metal complexes
<p>Supporting Information data for associated publication "Graph neural networks for predicting metal–ligand coordination of transition metal complexes".</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.