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1,084 results for “substrate”
Figure 1 in Muscidae (Diptera) of medico-legal importance associated with ephemeral organic substrates in seasonally dry tropical forests
Figure 1. Location of sample sites along the seasonally dry tropical forest (Caatinga) in Northeastern Brazil. (A) Petrolina; (B) Betânia; (C) Afogados da Ingazeira; (D) Buíque; (E) Boqueirão.
Figure 3 in Muscidae (Diptera) of medico-legal importance associated with ephemeral organic substrates in seasonally dry tropical forests
Figure 3. Cluster analysis for the similarity between muscid assemblages, according to the type of bait.
Figure 2 in Muscidae (Diptera) of medico-legal importance associated with ephemeral organic substrates in seasonally dry tropical forests
Figure 2. Sex ratio (female/male) of muscids collected in SDTF's fragments in Brazil, according to the type of bait (A) and species (B).
Supplementary Information for "Semi-automated high-throughput substrate screening assay for nucleoside kinases
<p>This is the external Supplementary Information for our publication "Semi-automated high-throughput substrate screening assay for nucleoside kinases". Files are to follow soon. We apologize for the delay. Thank you for your patience.</p> <p> </p> <p>The preprint and the Supporting Information are available at ChemRxiv (https://doi.org/10.33774/chemrxiv-2021-k0w7q).</p>
Deliverable 1.3 Growth of hBN via CVD as a high-mobility substrate
<p>The growth of hBN is explored via CVD on Ni, using a tubular reactor and ammonia borane as precursors. The parameter space was explored and hBN was successfully grown. This deliverable reports the recipe and growth of hBN via CVD, and a complete and extensive characterization with Optical Microscopy (OM), X-Ray Photoelectron Spectroscopy (XPS), Electron Energy Loss Spectra (EELS) and Transmission Electron Microscopy (TEM). Two different 10x10mm2 samples from different areas of a 4’ wafer sample were analysed by OM and XPS, and two other areas where transferred to TEM grids for TEM characterization (4 samples in total with complementary techniques).</p>
Figure 5. Unusual substrates. a-b, Immature P in Natural history of the agave jumping spider, Paraphidippus basalis (Araneae: Salticidae: Dendryphantina)
Figure 5. Unusual substrates. a-b, Immature P. basalis on a dead sotol leaf. c-d, Immature approximately two meters above ground level on a sotol inflorescence.
Simulations of Sec61 with a substrate-selective inhibitor
<p>Simulation inputs and outputs for manuscript "Signal peptide mimicry primes Sec61 for client-selective inhibition" by Rehan <em>et al</em>. Nature Chemical Biology 19, pages 1054–1062 (2023). DOI: 10.1038/s41589-023-01326-1.</p> <p>The Sec61 complex, embedded in a lipid bilayer mimicking ER in composition [1–4], was simulated in the presence ("Sec61_KZR8445", 5×1 µs) and absence ("Sec61_noinhibitor", 3×1 µs) of the cotransin KZR-8445 inhibitor. Additionally, a N300A mutant of Sec61α ("Sec61_KZR8445_N300A") was simulated in the presence of KZR-8445 for 1 µs. The replicas are labeled with "R". </p> <p>The GROMACS-compatible files include:</p> <ul> <li>Run input files (.tpr)</li> <li>Trajectory with coordinates written every 1 ns (.xtc)</li> <li>Energy file (.edr)</li> <li>Final coordinates after 1 µs of simulation (.gro)</li> <li>Continue points for extending the simulation (.cpt)</li> </ul> <p>Additionally, for each type of simulation (with KZR8445, without KZR8445, N300A mutation), common files are included:</p> <ul> <li>Index file (.ndx)</li> <li>Topology file (.top)</li> </ul> <p>The run parameter file (md.mdp) is common for all systems. The topologies (.itp) referred to by the top files are compressed into the TOP.tar archive.</p> <p><strong>Additional details on the methodology used in the simulations is described below:</strong></p> <p>We used the CHARMM36m protein force field [5,6], the CHARMM36 lipid force field [7], the CGenFF force field for the inhibitor with the ligand containing a positive dummy particle describing the bromobenzyl sigma hole [8,9], and CHARMM-specific TIP(S)3P model for water [10,11]. The systems were generated in CHARMM-GUI [12,13], including the protein positioning using PPM 2.0 [14] and the ligand parametrization within CHARMM-GUI [15].</p> <p>The leap-frog integrator was used with a time step of 2 fs. Buffered Verlet lists were used [16]. The Lennard-Jones forces were switched to zero between 1.0 and a cut-off distance of 1.2 nm. Long-range electrostatic interactions were included by the smooth particle mesh Ewald algorithm [17,18]. Temperatures of the protein (including the inhibitor), the lipids, and the solvent (water and ions) were separately coupled to a Nosé–Hoover thermostat [19,20] with a target temperature of 310 K and a relaxation time of 1 ps. The pressure was maintained at 1 bar with a semi-isotropic Parrinello–Rahman barostat [21]. The target pressure was set to 1 bar, the compressibility to 4.5 × 10<sup>–5</sup> bar<sup>–1</sup> and the relaxation time constant 5 ps. Bonds involving hydrogens were constrained with p-LINCS [22,23].</p> <p>[1] Bollen, I. C. & Higgins, J. A. Phospholipid asymmetry in rough- and smooth-endoplasmic-reticulum membranes of untreated and phenobarbital-treated rat liver. <em>Biochem. J</em> 189, 475–480 (1980).<br> [2] Colbeau, A., Nachbaur, J. & Vignais, P. M. Enzymac characterization and lipid composition of rat liver subcellular membranes. <em>Biochim. Biophys. Acta </em>249, 462–492 (1971).<br> [3] Davison, S. C. & Wills, E. D. Studies on the lipid composition of the rat liver endoplasmic reticulum after induction with phenobarbitone and 20-methylcholanthrene. <em>Biochem. J</em> 140, 461–468 (1974).<br> [4] Casares, D., Escribá, P. V. & Rosselló, C. A. Membrane Lipid Composition: Effect on Membrane and Organelle Structure, Function and Compartmentalization and Therapeutic Avenues. <em>Int. J. Mol.</em> Sci. 20, (2019).<br> [5] Huang, J. & MacKerell, A. D., Jr. CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. <em>J. Comput. Chem.</em> 34, 2135–2145 (2013).<br> [6] Huang, J. et al. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. <em>Nat. Methods</em> 14, 71–73 (2017).<br> [7] Klauda, J. B. et al. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. <em>J. Phys. Chem. B</em> 114, 7830–7843 (2010).<br> [8] Vanommeslaeghe, K. et al. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. <em>J. Comput. Chem.</em> 31, 671–690 (2010).<br> [9] Soteras Gutiérrez, I. et al. Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand-protein interactions. <em>Bioorg. Med. Chem.</em> 24, 4812–4825 (2016).<br> [10] Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. <em>J. Chem. Phys.</em> 79, 926–935 (1983).<br> [11] Durell, S. R., Brooks, B. R. & Ben-Naim, A. Solvent-Induced Forces between Two Hydrophilic Groups.<em> J. Phys. Chem.</em> 98, 2198–2202 (1994).<br> [12] Jo, S., Kim, T., Iyer, V. G. & Im, W. CHARMM-GUI: a web-based graphical user interface for CHARMM. <em>J. Comput. Chem</em>. 29, 1859–1865 (2008).<br> [13] Wu, E. L. et al. CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. <em>J. Comput. Chem.</em> 35, 1997–2004 (2014).<br> [14] Lomize, M. A., Pogozheva, I. D., Joo, H., Mosberg, H. I. & Lomize, A. L. OPM database and PPM web server: resources for positioning of proteins in membranes. <em>Nucleic Acids Res. 40</em>, D370–6 (2012).<br> [15] Kim, S. et al. CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules. <em>J. Comput. Chem.</em> 38, 1879–1886 (2017).<br> [16] Páll, S. & Hess, B. A flexible algorithm for calculating pair interactions on SIMD architectures. <em>Comput. Phys. Commun.</em> 184, 2641–2650 (2013).<br> [17] Darden, T., York, D. & Pedersen, L. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. <em>J. Chem. Phys.</em> 98, 10089–10092 (1993).<br> [18] Essmann, U. et al. A smooth particle mesh Ewald method. <em>J. Chem. Phys.</em> 103, 8577–8593 (1995).<br> [19] Nosé, S. A unified formulation of the constant temperature molecular dynamics methods. <em>J. Chem. Phys.</em> 81, 511–519 (1984).<br> [20] Hoover, W. G. Canonical dynamics: Equilibrium phase-space distributions. <em>Phys. Rev. A Gen. Phys.</em> 31, 1695–1697 (1985).<br> [21] Parrinello, M. & Rahman, A. Polymorphic transitions in single crystals: A new molecular dynamics method. <em>J. Appl. Phys.</em> 52, 7182–7190 (1981).<br> [22] Hess, B. P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation. <em>J. Chem. Theory Comput.</em> 4, 116–122 (2008).<br> [23] Hess, B., Bekker, H., Berendsen, H. J. C. & Fraaije, J. G. E. M. LINCS: A linear constraint solver for molecular simulations. <em>J. Comput. Chem.</em> 18, 1463–1472 (1997).</p>
Raw data for the article "Substrate-Controlled C-H or C-C Alkynylation of Cyclopropanes: Generation of Aryl Radical Cations by Direct Light Activation of Hypervalent Iodine Reagents "
<p>Raw computational, NMR, IR and MS data for the article "Substrate-Controlled C-H or C-C Alkynylation of Cyclopropanes: Generation of Aryl Radical Cations by Direct Light Activation of Hypervalent Iodine Reagents " published in Chemical Science, DOI: </p> <p><a href="https://doi.org/10.1039/D2SC04344K">https://doi.org/10.1039/D2SC04344K</a></p> <p>The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article.</p>
Refractive index sensitivity of scattering by Al-PAAO-Au film substrates
<p>Project: Nanostructured multilayer hybrid coatings for interferometric and optoelectronic sensors (LZP-2020/1-0200)</p>
A neural substrate for negative affect dictates female parental behaviour.
<p># Abstract</p> <p>Parental behaviours are essential to secure survival and wellbeing of newborns. Concomitantly, parenting also limits negative affective states in adults, which emerge when the coping with neonatal distress becomes a challenge. Whether neural circuits that process negative affect orchestrate components of parental behaviours remains, however, unknown. Here, we identify functional and transcriptional signatures of parental behaviours in neurons of the negative emotion center lateral habenula receiving bed nucleus of the stria terminalis innervation (BNSTLHb). Calcium imaging and optogenetic manipulations reveal that LHb neurons of virgin female mice increase their activity in response to pup distress vocalization and are necessary for pup calls-driven aversive behaviours. Accordingly, LHb activity rises during the retrieval of a pup to a nest, a behaviour worsened by optogenetic LHb inactivation. Intersectional cell identification and transcriptional profiling associates the BNSTLHb neuronal population to parental behaviours and outlines gene expression in female virgins that is similar to mothers but divergent from non-parental virgin male mice. Accordingly, optogenetic activation and inactivation of the BNST-LHb pathway maximizes and suppresses, respectively, the parental behaviour. Finally, tracking and manipulating single BNSTLHb cell activity demonstrates specificity of this neuronal subset for encoding negative affect and pup retrieval, but not sociability amongst conspecifics. Thus, BNSTLHb cells are operational for female parenting, demonstrating that a negative affect neural circuit processes newborn distress signals and limits them through female parenting.</p> <p> </p> <p># Files available to generate figures.</p> <p>- Fastq Files : Raw reads output</p> <p>Alignment of sequenced reads to the mouse genome (GRCm38) and filtered gene–barcode matrices were realized by running Cell Ranger Single-Cell Software Suite v5.0.1 (10X Genomics).</p> <p>The cell ranger count function was used to generate filtered gene/cell expression UMI corrected matrices by selecting probable nuclei and removing empty lipid droplets.</p> <p>Command line use for cell ranger /opt/cellranger-5.0.1/cellranger count --id=MAc --transcriptome=/refgenome/refdata-gex-mm10-2020-A --libraries=library.csv --expect-cells=2000 --include-introns --localcores=20 --localmem=32</p> <p>MAc_S1_L001_R1_001.fastq.gz<br> MAc_S1_L001_R2_001.fastq.gz<br> MBc_S1_L001_R1_001.fastq.gz<br> MBc_S1_L001_R2_001.fastq.gz<br> MCc_S1_L001_R1_001.fastq.gz<br> MCc_S1_L001_R2_001.fastq.gz</p> <p><br> - src.src R script to reproduce analysis.<br> - source.src R source script containing useful functions.</p> <p>- singlecell_countmatrix.tsv.gz: is a count matrix in tab-separated format. It contains the result of the single cell quantification for all genes and all cells after QC. The values represent the number of exonic reads mapping into each gene after UMI correction. The first columns contain the gene name that is quantified.</p> <p>- singlecell_metadata.tsv: is a table containing metadata information for each cells analyse in the paper in tab-separated. </p> <p>- all_umap.Rds Secondary processed file use in the script.<br> - habenula.integrated.Rds Secondary processed file use in the script containing external dataset use in this analysis.</p>
Figure 5. Different substrates where L in Leiosolenus (Labis) patagonicus (Bivalvia: Mytilidae) from Argentinean sea, taxonomic revision and anatomical notes
Figure 5. Different substrates where L. patagonicus can be sampled. (A-B) Aulacomya atra (MACN-29479); (C) Corallinacea algae; (D-E) Ameghinomya antiqua (P.P. King, 1832) (CNP-INV 2877); (F-H) Ostrea puelchana d′Orbigny, 1844 (CNP-INV 2877); (I) sedimentary rock with tubes (CNP-INV 2877); (J-K) detail of tubes (CNP-INV 2864).
The roles of phylogeny, body size and substrate use in trabecular bone variation among Philippine 'earthworm mice' (Rodentia: Chrotomyini)
<p>Trabecular bone is modelled throughout an animal's life in response to its mechanical environment, but like other skeletal anatomy, it is also subject to evolutionary influences. Yet the relative strengths of factors that affect trabecular bone architecture are little studied. We investigated these influences across the Philippine endemic murine rodent clade Chrotomyini. These mammals have robustly established phylogenetic relationships, exhibit a range of well-documented substrate-use types, and have a body size range spanning several hundred grammes, making them ideal for a tractable study of extrinsic and intrinsic influences on trabecular bone morphology.</p> <p>We found slight differences in vertebral trabecular bone among different substrate-use categories, with more divergent characteristics in more ecologically specialized taxa. This suggests that the mechanical environment must be relatively extreme to affect trabecular bone morphology in small mammals. We also recovered allometric patterns that imply that selective pressures on bone may differ between small and large mammals. Finally, we found high intrataxonomic variation in trabecular bone morphology, but it is not clearly related to any variable we measured, and may represent a normal degree of variation in these animals rather than a functional trait. Future studies should address how this plasticity affects biomechanical properties and performance of the skeleton.</p>
datasets for A systematic approach to study protein-substrate specificity enables the identification of Ssh1 substrate range
<p>datasets for A systematic approach to study protein-substrate specificity enables the identification of Ssh1 substrate range</p>
Data for: Ambient and substrate energy influence decomposer diversity differentially across trophic levels
<p><span>The species-energy hypothesis predicts increasing biodiversity with increasing energy in ecosystems. Proxies for energy availability are often grouped into ambient energy (i.e., solar radiation) and substrate energy (i.e., non-structural carbohydrates or nutritional content). The relative importance of substrate energy is thought to decrease with increasing trophic level from primary consumers to predators, with reciprocal effects of ambient energy. Yet, empirical tests are lacking. We compiled data on 332,557 deadwood-inhabiting beetles of 901 species reared from wood of 49 tree species across Europe. Using host-phylogeny-controlled models, we show that the relative importance of substrate energy versus ambient energy decreases with increasing trophic levels: the diversity of zoophagous and mycetophagous beetles was determined by ambient energy, while non-structural carbohydrate content in woody tissues determined that of xylophagous beetles. Our study thus overall supports the species-energy hypothesis and specifies that the relative importance of ambient temperature increases with increasing trophic level with opposite effects for substrate energy.</span></p>
Data from: Insights into the Genomics of Clownfish Adaptive Radiation: the Genomic Substrate of the Diversification
<p>Mitochondrial genome assembly of 9 clownfish (<strong><em>Amphiprion akallopisos, A. bicinctus, A. melanopus, A. nigripes, A. ocellaris, A. preideraion, A. polymnus, A. sebae, Premnas biaculeatus</em>)</strong> species and 1 damselfish species (<strong><em>Pomacentrus moluccensis</em></strong>), presented in "Insights into the genomics of clownfish adaptive radiation: the genomic substrate of the diversification". </p>
Expulsion mechanism of the substrate-translocating subunit in ECF transporters
<p>Data for coarse-grained molecular dynamics simulations (final snapshots, cleaned trajectories, starting structure/simulation parameters) described in "Expulsion mechanism of the substrate-translocating subunit in ECF transporters".</p>
Concentrations and isotope ratios of N2O and related substrates with hydrographical data obtained in the eastern Indian Ocean in November, 2018
<p>A spreadsheet that includes data presented in the following publication.</p> <p>Sakae Toyoda, Kotaro Terajima, Naohiro Yoshida, Chisato Yoshikawa, Akiko Makabe, Fuminori Hashihama, and Hiroshi Ogawa, Extensive Accumulation of Nitrous Oxide in the Oxygen Minimum Zone in the Bay of Bengal, Global Biogeochemical Cycles, accepted for publication on August 8, 2023.</p>
Data for "Transparent Porous Conductive Substrates for Gas-Phase Photoelectrochemical Hydrogen Production"
<p>Data archive for "Transparent Porous Conductive Substrates for Gas-Phase Photoelectrochemical Hydrogen Production"</p> <p>DOI: 10.1002/adma.202208740</p>
FIG. 4 in Bryophyte colonization on the monuments of Champaner Pavagadh - UNESCO World Heritage Site and its association with geological substrates
FIG. 4. — Quantitative representation of species colonization on Champaner Pavagadh monuments.
Data from: leaf functional diversity and environmental filtering in a tropical dry forest: comparison between two geological substrates
<p><span>The role of geological substrate in shaping plant community functional diversity remains poorly understood. Considering the involvement of leaves in the energy, water and nutrient economics of plants, we hypothesized that leaves experience geology-related filtering, impacting functional attributes and functional leaf community diversity on different substrates. We studied tropical dry forest communities on limestone and siliciclastic phyllite-derived soils, comparing their functional diversity and soil physico-chemical properties. We predicted the most benign habitat (less severe filter) to be associated with higher leaf functional diversity and an acquisitive strategy prevalence, while the more stressful habitat should show conservative leaf traits and lower leaf functional diversity. We measured six traits in 31 common tree species (representing ~80% of community crown cover): leaf area, specific leaf area, leaf thickness, leaf dry matter content, petiole length, and leaf blade narrowness. Leaf functional diversity was assessed through the functional trait dispersion metric. Intraspecific functional variation was examined in 25 species shared between substrates. The limestone substrate was more fertile (higher phosphorous) with higher water retention, while phyllite had higher nitrogen and lower humidity. Principal component analysis segregated plots by substrate, with limestone plots being more clustered. Community leaf functional diversity was higher in the limestone forest. Most species examined showed inter-substrate trait differences in at least one leaf functional trait. The two substrates constituted distinct growth environments, with the more benign substrate associated to higher community functional leaf diversity. The intraspecific analysis revealed the prevalence of acquisitive traits in the more benign and more conservative traits in the more stressful habitat. This study advances our understanding of the role of geological substrate as an environmental filter in tropical dry forest, influencing leaf functional responses and emphasizing the importance of intraspecific functional variation.</span></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
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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.
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