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236 results for “active site”
Data from: Reactive high-spin iron(IV)-oxo sites through dioxygen activation in a metal–organic framework
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Survey 200 long term study of multiple sites in central Arizona-Phoenix: human activity related measurements
The Ecological Survey of Central Arizona (ESCA) is an extensive field survey and integrated inventory designed to capture key ecological indicators of the CAP LTER study area consisting of the urbanized, suburbanized, and agricultural areas of metropolitan Phoenix, and the surrounding Sonoran desert. The survey is conducted every five years at approximately 200 sample plots (30m x 30m) that were located randomly using a tessellation-stratified dual-density sampling design. Study plots cover habitats throughout the CAP LTER study area ranging from native Sonoran desert sites to residential yards to an airport tarmac. Measurements include an inventory of all plants (identified to the lowest possible taxonomic unit, typically species), plant biovolume, soil coring for physicochemical properties, arthropod sweep-net sampling, photo documentation, and a visual survey of site and area characteristics. The objectives of the survey are to (1) characterize patches in terms of key biotic, physical, and chemical variables, and (2) examine relationships among land use, general plant diversity, native plant diversity, plant biovolume, soil nutrient status, and social-economic indices along an indirect urban gradient. Survey 200 was the original name of the project, and it was renamed to ESCA following the survey conducted in 2015. The data set here includes a subset of information from the Survey200/ESCA focusing exclusively on buildings and indicators of human activity in the survey plots. Investigators interested in more recent survey data, or other variables measured as part of ESCA should search the data catalog for 'ecological survey of central arizona' or 'survey 200'.
Data from: Late Neolithic phytolith and charcoal records of human activities and vegetation change in Shijiahe culture, Tanjialing site, China
There is significant archaeological evidence marking the collapse of the Shijiahe culture in the middle reaches of the Yangtze River in China during the late Neolithic Period. However, the causes for this cultural collapse remain unclear. Our sedimentary records from a 3.3 m long profile and 76 phytolith and charcoal samples from the Tanjialing archaeological sites provide records of interactions between an ancient culture and vegetation change. During the early Shijiahe culture (c, 4850-4400 cal BP), the climate was warm and humid. Fire was intensively used to clear the vegetation. In the mid-period of the Shijiahe culture (c, 4400-4200 cal BP), the climate became slightly dry-cold and this was accompanied by decreasing water, leading to settlements. From c, 4200 cal BP, severe drought eroded the economic foundation of rice-cultivation. These conditions forced people to abandon the Shijiahe ancient city to find water in other regions, leading to the collapse of the Shijiahe culture.
Data file for paper: " In situ electrochemical quantification of active sites in Fe–N/C non-precious metal catalysts.", Nature. Communications, 7, 13285 doi: 10.1038/ncomms13285 (2016).
<p>The data in this spreadsheet was used to produce the figures in the paper</p> <p>Malko, D., Kucernak, A and Lopes, T, " In situ electrochemical quantification of active sites in Fe–N/C non-precious metal catalysts." </p> <p>Nat. Commun., 7, 13285 doi: 10.1038/ncomms13285 (2016).</p> <p>Please cite the above reference if you wish to use this data</p>
Sequence-independent, site-specific incorporation of chemical modifications to generate light-activated plasmids (Source Data)
<p>Source data for Chemical Science paper "Sequence-independent, site-specific incorporation of chemical modifications to generate light-activated plasmids" DOI: 10.1039/D3SC02761A</p>
Supporting data set for: Sulfur-deficient edges as active sites for hydrogen evolution on MoS2
<p>Computed structures of the elementary steps of hydrogen evolution on MoS2 edges and basal plane, obtained with neutral supercells.</p><p>Naming convention: POSCAR-[system]-[number of H after Volmer step]-[reaction]-[state].</p>
Molecular dynamics results of the complex 3CLpro active site with compound 5
<p>Molecular dynamics results of the complex 3CLpro active site with compound <strong>5</strong>. The protein structure is shown in gray and the compound <strong>5</strong> is shown in orange.</p>
No bridge between us: EXAFS and computations confirm two distant iron ions comprise the active site of alkane monooxygenase (AlkB)
<p>This dataset contains computational data for the paper "No bridge between us: EXAFS and computations confirm two distant iron ions comprise the active site of alkane monooxygenase (AlkB)". All computations in this repository were performed by Clorice Reinhardt, a Arnold O. Beckman Postdoctoral Fellow in the Chemical Sciences in Prof. Heather Kulik's lab at MIT, and EXAFS data uploaded was analyzed and prepared for this repository by Christopher J. Pollock</p>
Characterization of Site-Specific Vegetation Activity in Alaskan Wet and Dry Tundra as Related to Climate and Soil State DATA
<p>We present discrete (2-hour resolution) multi-year (2008 – 2017) <em>in situ </em>measurements of seasonal vegetation growth and soil biophysical properties from two sites on Alaska’s North Slope, USA, representing dry and wet sedge tundra. We examine measurements of vertical active soil layer temperature and soil moisture profiles (freeze/thaw status), woody shrub vegetation physiological activity, and meteorological site data to assess interrelationships within (and between) these two study sites.</p> <p>Vegetation phenophases (cold de-hardening start, physiological function start, stem growth start, stem growth end, physiological function end, cold hardening completion) were found to have greater inter-annual Day-Of-Year (DOY) occurrence variability at the dry site compared to the wet site. At the dry site, vegetation activity begins on average ~ 7 days earlier and ends ~ 11 days earlier. The mean active stem growth window lasts ~ 54 days for the dry site and ~51 days for the wet site. Vegetation, in both tundra environments, began cold de-hardening functions (warm season prep) prior to atmospheric temperatures warming above 0°C. Similar results were found related to the critical soil freeze/thaw/transition dates; the dry site had a DOY phenophase occurrence range that was 8 days larger than that of the wet site. A longer continuous summer thaw period was captured at the wet site by ~ 26 days throughout the active layer. In addition, the dry site was measured to have longer spring and fall soil isothermal conditions than the wet site by ~ 9 and 5 days throughout the active layer. These results show that the dry site’s willow shrub vegetation physiology and soil condition phenology is more variable than the wet site.</p> <p>Alongside the <em>in situ</em> data, a remote sensing product from NASA’s MEaSUREs program was utilized; our research indicates that the AMSR derived satellite product is more precise over the wet tundra site with critical date alignment between remote sensing observations and <em>in situ</em> measurements ranging from ~ 4 to 11 days. Furthermore, the AMSR product was shown to preemptively estimate land surface condition change during the spring transition for both tundra types while lagging during the fall transition and freeze-up periods.</p>
The datasets for the paper "Spatial and temporal distribution of lobate scarps in the lunar south polar region: Evidence for latitudinal variation of scarp geometry, kinematics and formation ages, continuous tectonic activity in the last 100 million years and seismically safe south pole Artemis human landing site" Geophysical Research Letters.
<p>This dataset provides the original data that were used for preparing the illustrations, figures and tables.</p>
Structural Dynamics Support Electrostatic Interactions in the Active Site of Adenylate Kinase - V142G mutant
<p>Tinker MD trajectories of AdK WT and mutants as described in the paper published in ChemBioChem, e202200097.</p>
Structural Dynamics Support Electrostatic Interactions in the Active Site of Adenylate Kinase - A55G and V135G mutants
<p>Tinker MD trajectories of AdK WT and mutants as described in the paper published in ChemBioChem, e202200097.</p>
Experimental and Computational Study Towards Identifying Active Sites of Supported SnOx Nanoparticles for Electrochemical CO2 Reduction Using Machine-Learned Interatomic Potentials
<p>SnOx has received great attention as an electrocatalyst for CO2 reduction reaction (CO2RR), however, it still suffers from low activity. Moreover, the atomic-level SnOx structure and the nature of the active sites are still ambiguous due to the dynamism of surface structure and difficulty in structure characterization under electrochemical conditions. Herein, we first enhance its CO2RR performance by supporting SnO2 nanoparticles on two common supports, Vulcan Carbon and TiO2 . Then, electrolysis of CO2 at various temperatures in a neutral electrolyte reveals that the application window for this catalyst is between 12 and 30 °C.<br>Furthermore, our study introduces a machine learning interatomic potential method for the atomistic simulation to investigate SnO 2 reduction and establish a correlation between SnO x structures and their CO 2 RR performance. In addition, selectivity is analyzed computationally with density functional theory simulations to identify the key differences between the binding energies of *H and *CO2−, where both are correlated with the presence of oxygen on the nanoparticle surface. This study offers in-depth insights into the rational design and application of SnOx -based electrocatalysts for CO2RR.</p>
Mayorov et al - Scripts and tables with psychoprot descriptor information for active and "non-active" sites
<p>These are the scripts used in our work; and the tables from Jack et al PLoS Biol 2016 extended with descriptor information from psychoprot fits for active and "non-active" sites.</p>
Dataset for the paper "Oxygen reduction reaction activity in non-precious single atom (M-N/C) catalysts – contribution of metal and carbon/nitrogen framework-based sites", 2023, ACS Catalysis, DOI:10.1021/acscatal.3c00356
<p>The data in this spreadsheet was used to produce the figures in the paper</p> <p>Authors:Mengjun Gong, Asad Mehmood, Basit Ali, Kyung-Wan Nam and Anthony Kucernak</p> <p>Title:Oxygen reduction reaction activity in non-precious single atom (M-N/C) catalysts – contribution of metal and carbon/nitrogen framework-based sites</p> <p>Journal:ACS Catalysis</p> <p>DOI:10.1021/acscatal.3c00356</p> <p>Please cite the above reference if you wish to use this data</p> <p>DOI of data:10.5281/zenodo.7879881</p>
Renewable energies and biodiversity: impact of ground-mounted solar photovoltaic sites on bat activity
<ol> <li>Renewable energy is growing at a rapid pace globally, but as yet there has been little research on the effects of ground-mounted solar photovoltaic (PV) developments on bats, many species of which are threatened or protected.</li> <li>We conducted a paired study at 19 ground-mounted solar PV developments in southwest England. We used static detectors to record bat echolocation calls from boundaries (i.e., hedgerows) and central locations (open areas) at fields with solar PV development, and simultaneously at matched sites without solar PV developments (control fields). We used generalized linear mixed-effect models to assess how solar PV developments and boundary habitat affected bat activity and species richness.</li> <li>The activity of six of eight species/species groups analysed was negatively affected by solar PV panels, suggesting that loss and/or fragmentation of foraging/commuting habitat is caused by ground-mounted solar PV panels. <em>Pipistrellus</em> <em>pipistrellus</em> and <em>Nyctalus</em> spp. activity was lower at solar PV sites regardless of the habitat type considered. Negative impacts of solar PV panels at field boundaries were apparent for the activity of <em>Myotis</em> spp. and <em>Eptesicus</em> <em>serotinus</em>, and in open fields for <em>Pipistrellus</em> <em>pygmaeus</em> and <em>Plecotus</em> spp.</li> <li>Bat species richness was greater along field boundaries compared with open fields, but there was no effect of solar PV panels on species richness.</li> <li> <em>Policy Implications</em>: Ground-mounted solar PV developments have a significant negative effect on bat activity, and should be considered in appropriate planning legislation and policy. Solar PV developments should be screened in Environmental Impact Assessments for ecological impacts, and appropriate mitigation (e.g., maintaining boundaries, planting vegetation to network with surrounding foraging habitat) and monitoring should be implemented to highlight potential negative effects.</li> </ol>
Fig. 7 in The CYP74B and CYP74D divinyl ether synthases possess a side hydroperoxide lyase and epoxyalcohol synthase activities that are enhanced by the site-directed mutagenesis
Fig. 7. The unrooted phylogenetic tree of the CYP74 family. Classified CYP74 subfamilies are marked with their letter designations (A, B, C, etc.). Subfamilies consisting of more than one member are outlined with unclosed curves (semi-ellipses). The following CYP74s were used for analysis: As, A. sativum; AsDES (CYP74H1), CAI30435.1; At, Arabidopsis thaliana; AtAOS (CYP74A1), NP199079.1; AtHPL (CYP74B2), C74B2ARATH; Ca, C. annuum; CaHPL (CYP74B1), NP001311810.1; CaDES (CYP74D4), NP001311513.1; Cas, Camellia sinensis; CasHPL (CYP74B24), BAU24783.1; Cs, Cucumis sativus; CsHPL/EAS/AOS (CYP74C31), XP004137005.1; CsHPL/EAS (CYP74C1_Cs), NP001274399.1; Cm, Cucumis melo; CmHPL/EAS (CYP74C2), NP001284390.1; Dc, Daucus carota; DcAOS (CYP74B33), XP_017248700.1; Gm, G. max; GmAOS (CYP74A1), NP001236432.1; GmHPL/EAS (CYP74C13_Gm), KRH29541.1; Hv, Hordeum vulgare, HvAOS2 (CYP74A3), CAB86384.1; Le, L. esculentum; LeAOS1 (CYP74A1), CAB88032.1; LeAOS2 (CYP74A2), AAF67141.1; LeAOS3 (CYP74C3), NP001265949.1; LeHPL (CYP74B3), AAF67142.1; LeDES (CYP74D1), NP001234527.1; Lu, L. usitatissimum; LuAOS (CYP74A1), sp|P48417.1; LuDES (CYP74B16), ADP03054.2; Mp, M. polymorpha, MpAOS1, BAS32647.1; MpAOS2, BAS32648.1; Mt, Medicago truncatula; MtHPL/EAS (CYP74C13_Mt), XP003606860.1; MtHPL3 (CYP74B4), AAY30368.1; Nt, N. tabacum; NtDES (CYP74D3), NP001312606.1; Os, Oryza sativa; OsAOS1 (CYP74A4), XP015631686.1; OsHPL2 (CYP74E1), EAY85033.1; Pa, Parthenium argentatum; PaAOS (CYP74A1), sp| Q40778.2; Pd, Prunus dulcis; PdHPL (CYP74C5), CAE18065.1; Pg, Psidium guajava; PgHPL (CYP74B5), AAK15070.1; Pi, Petunia inflata; PiCYP74C9, ABC75838.1; Pp, P. patens; PpAOS1 (CYP74A1), XP024380613.1; PpAOS2 (CYP74A8), XP024372097.1; PpHPL (CYP74G1), CAC86920.2; Ra, R. acris; RaDES (CYP74Q1), AJU57209.1; Rj, R. japonicus; RjEAS (CYP74A88), QCR70269.1; Sm, S. moellendorffii; SmDES1 (CYP74M1), XP002979266.1; SmDES2 (CYP74M3), XP002964012.2; SmEAS (CYP74M2), EFJ26024.1; St, S. tuberosum; StAOS2 (CYP74A6), ABD15175.1; StAOS3 (CYP74C10), CAI30876.1; StHPL/EAS (CYP74C4), XP006365486.1; StDES (CYP74D2), NP001305517.1; Zm, Zea mays; ZmAOS1 (CYP74A19), AAR33048.1; ZmHPL (CYP74F2), NP_001105255.2. The multiple alignments of selected CYP74 amino acid sequences and phylogenetic tree building were made with MEGA7 software. Multiple alignment was performed using the ClustalW method, phylogenetic tree was build using the maximum likelihood method based on the Poisson correction model (Zuckerkandl and Author- Anonymous, 1965); the bootstrap consensus tree was inferred from 1000 replicates (Felsenstein, 1985). The analysis involved 45 amino acid sequences.
Fig. 6 in The CYP74B and CYP74D divinyl ether synthases possess a side hydroperoxide lyase and epoxyalcohol synthase activities that are enhanced by the site-directed mutagenesis
Fig. 6. The mechanisms of fatty acid hydroperoxide conversions by target DESs. R = HOOC(CH2)7–, R' = n-butyl.
Fig. 4 in The CYP74B and CYP74D divinyl ether synthases possess a side hydroperoxide lyase and epoxyalcohol synthase activities that are enhanced by the site-directed mutagenesis
Fig. 4. GC-MS analyses of products (Me/TMS) of recombinant WT LuDES incubations with 9(S)-HPOD (A), 9(S)-HPOT (B), 13(S)-HPOD (C), and 13(S)- HPOT (D). 2, 9,10-epoxy-11-hydroxy-12-octadecenoic acid (Me/TMS); 3, 9- hydroxynonanoic acid (Me/TMS); 5, 9,10-epoxy-11-hydroxy-12,15-octadecadienoic acid (Me/TMS); 6, 11-hydroxy-12,13-epoxy-9-octadecenoic acid (Me/ TMS); 7, (ω5Z)-etherolenic acid (Me); 8, (9Z)-12-hydroxy-9-dodecenoic acid (Me/TMS); 9, (10E)-12-hydroxy-10-dodecenoic acid (Me/TMS); 10, 11-hydroxy-12,13-epoxy-9,15-octadecadienoic acid (Me/TMS); 12, 9-hydroxy- 12,13-epoxy-10-octadecenoic acid (Me/TMS); 13, 9,10-epoxy-13-hydroxy- 11,15-octadecadienoic acid (Me/TMS); 14, 9,10-epoxy-13-hydroxy-11-octadecenoic acid (Me/TMS). The structural formulae of products are presented in Fig. 2. 9-HOD/T and 13-HOD/T are decrypted in Fig. 3.
Fig. 3 in The CYP74B and CYP74D divinyl ether synthases possess a side hydroperoxide lyase and epoxyalcohol synthase activities that are enhanced by the site-directed mutagenesis
Fig. 3. GC-MS analyses of products (Me/TMS) of recombinant NtDES incubations with 9(S)-HPOD (A), 9(S)-HPOT (B), 13(S)-HPOD (C), and 13(S)- HPOT (D). 1, colneleic acid (Me); 2, 9,10-epoxy-11-hydroxy-12-octadecenoic acid (Me/TMS); 3, 9-hydroxynonanoic acid (Me/TMS); 4, colnelenic acid (Me); 4a, (3′E)-colnelenic acid (Me); 6, 11-hydroxy-12,13-epoxy-9-octadecenoic acid (Me/TMS). The structural formulae of products are presented in Fig. 2. 9-HOD, (9S,10E,12Z)-9-hydroxy-10,12-octadecadienoic acid; 9-HOT, (9S,10E,12Z,15Z)-9-hydroxy-10,12,15-octadecatrienoic acid; 13-HOD, (9Z,11E, 13S)-13-hydroxy-9,11-octadecadienoic acid; 13-HOT, (9Z,11E,13S,15Z)-13- hydroxy-9,11,15-octadecatrienoic acid.
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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.