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7,324 results for “pathways”
Dataset: 800 QM/MM minimum energy pathway conformations for the acylation reactions of Toho-1/ampicillin and Toho-1/cefalexin
<p>This dataset consists of 800 coordinate files (in the CHARMM psf/cor format) for the QM/MM minimum energy pathways of the acylation reactions between a Class A beta-lactamases (Toho-1) and two beta-lactam antibiotic molecules (ampicillin and cefalexin).</p> <p>These files are:</p> <ul> <li>toho_amp.r1-ae.zip: The R1-AE acylation pathways for Toho-1/Ampicillin (200 pathways);</li> <li>toho_amp.r2-ae.zip: The R2-AE acylation pathways for Toho-1/Ampicillin (200 pathways);</li> <li>toho_cex.r1-ae.zip: The R1-AE acylation pathways for Toho-1/Cefalexin (200 pathways);</li> <li>toho_cex.r2-ae.zip: The R2-AE acylation pathways for Toho-1/Cefalexin (200 pathways);</li> <li>energies.zip: the replica energies at B3LYP-D3/6-31+G**/C36 level;</li> <li>chelpgs.zip: the ChElPG charges of all reactant replicas at B3LYP-D3/6-31+G**/C36 level;</li> <li>farrys.zip: the featurzied NumPy arrays for model training;</li> <li>peephole.zip: an example file for how the optimized MEPs look like; </li> <li>dftb3_benchmark.zip: the reference calculations to justify the use of DFTB3/3OB-F/C36 in MEP optimizations, the reference level of theory is B3LYP-D3/6-31G**/C36. </li> </ul> <p>The R1-AE pathways are the acylation uses Glu166 as the general base; the R2-AE pathways uses Lys73 and Glu166 as the concerted base. </p> <p>All QM/MM pathways are optimized at the DFTB3/3OB-f/CHARMM36 level of theory. </p> <p>Z. Song et al Mechanistic Insights into Enzyme Catalysis from Explaining Machine-Learned Quantum Mechanical and Molecular Mechanical Minimum Energy Pathways. <em>ACS Phys. Chem Au</em> 2022, <strong>2</strong>, 4, 316–330. DOI: <a href="https://doi.org/10.1021/acsphyschemau.2c00005">10.1021/acsphyschemau.2c00005</a></p>
A dataset of bird assemblages in different successional pathways– a comparative study in hemiboreal mixed forests
<p><strong>Abstract:</strong></p> <p><strong>Context </strong>The most productive forest lands have naturally the richest bird assemblages but tend to be also most intensively managed. Sustainable solutions to this conflict are unclear.</p> <p><strong>Aim </strong>To assess bird assemblages and their successional dynamics in planted Norway spruce (<em>Picea abies </em>L.) stands compared to naturally developing stands.</p> <p><strong>Methods </strong>We mapped breeding bird assemblages in forty 5-ha plots on highly productive soils in Estonia. The plots included sets of naturally regenerated and planted stands, and (as successional endpoints) clear-cuts and old stands.</p> <p><strong>Results </strong>Planted stands had fewer bird species and pairs than naturally regenerated stands; the latter having a species composition resembling late-successional deciduous-dominated stands. Importantly, the species composition in mature spruce plantations converged toward the composition observed in late-successional conifer-dominated stands. Downed dead wood, stand age, deciduous trees, and stock density were the most significant stand characteristics shaping bird assemblages.</p> <p><strong>Conclusion</strong> The habitat value of established spruce plantations can be primarily improved by allowing for some deciduous trees and gaps with deciduous undergrowth. At the landscape scale, the bird diversity of even-aged systems would be enhanced by multi-scale applications of retention forestry – from retention trees to old-growth set-asides.</p> <p> </p> <p> </p> <p>The given dataset includes observations of breeding pairs on all 40 study plots with different management types. Variables explained in supplementary txt file. </p> <p> </p>
Fig. 2 in Circulation Pathways Of Trematodes Of Freshwater Gastropod Mollusks In Forest Biocenoses Of The Ukrainian Polissia
Fig. 2. Two-host life cycles of trematodes: а — alternation hosts; b — proportion of different classes of definitive hosts in life cycles.
Fig. 3 in Circulation Pathways Of Trematodes Of Freshwater Gastropod Mollusks In Forest Biocenoses Of The Ukrainian Polissia
Fig. 3. Three-host life cycle of trematodes: А — second intermediate hosts are aquatic invertebrates; В — second intermediate hosts are amphibiontic invertebrates; С — second intermediate hosts are vertebrates; а — alternation hosts; b — biological structure of helminth fauna.
EWINA_IPATHS : a global database of earthworm introductions' pathways into the US from 1945 to 1975
<p><strong>This dataset centralizes data of earthworm interception events at the US borders between 1945 and 1975.</strong></p> <p>These data come from the U.S. Bureau of Plant Quarantine, U.S. Department of Agriculture and were compiled by E. Gates in a list of papers (see references).</p> <p>Each record in the EWINA_IPATHS database relates an interception event of introduced earthworms.</p> <p>Interception events are described by the name of the intercepted species, its abundance, the date and place of interception, the geographical point of origin, the transportation mode (boat, plane, car), and the substrate in which the earthworms were found (e.g. soil, leaves, fish bait).</p> <p>EWINA_IPATHS contains 1 016 events of earthworm interceptions.</p> <p>Files:</p> <ul> <li><strong>EWINAPATH.csv </strong>: dataset itself</li> <li><strong>EWINAPATH_references.csv</strong> : list of references where the data come from. Merge to EWINAPATH.csv with the field source_ID.</li> <li><strong>EWINAPATH_variables.csv</strong>: list of variables and their meaning.</li> </ul> <p> </p> <p> </p>
Paulinella micropore KR01 manually corrected gene models from selected KEGG pathways
<p>Major results files produced from the analysis of the nucleotide biosynthesis, DNA replication, and histidine metabolism pathways in <em>Paulinella micropore</em> KR01.</p> <p> </p> <p><code>manually_corrected_genes.genome.gff3.gz</code></p> <p>Gene models (in GFF3 format) of manually corrected <em>P. micropora</em> KR01 genes.</p> <p> </p> <p><code>manually_corrected_genes.cds.fna.gz</code></p> <p>CDS of manually corrected <em>P. micropora</em> KR01 genes.</p> <p> </p> <p><code>manually_corrected_genes.pep.faa.gz</code></p> <p>Protein sequences of manually corrected <em>P. micropora</em> KR01 genes.</p> <p> </p> <p><code>fasta.tar.gz</code></p> <p>Sequences used for phylogenetic analysis of major KEGG Orthologs from the nucleotide biosynthesis, DNA replication, and histidine metabolism pathways.</p> <p> </p> <p><code>aln.tar.gz</code></p> <p>Alignments produced by <code>mafft</code> v7.453 (‘--localpair --maxiterate 1000’) that were used for phylogenetic analysis of the major KEGG Orthologs.</p> <p> </p> <p><code>tree.tar.gz</code></p> <p>Consensus trees produced by <code>iqtree</code> v1.6.12 (‘-m LG+R7 -bb 2000 -quiet’) that were used for phylogenetic analysis of the major KEGG Orthologs.</p>
Figures 1–6 in Identification of a potential pathway of the exotic black weevil (Coleoptera: Curculionidae) in South Korea
Figures 1–6. Black weevil (Aclees taiwanensis Kôno), NJ tree and regional map of South Korea. 1–2) Adult weevil on a fig tree. 3) Adult, dorsal view (JN: 1042 Aphae-ro, Aphae-eup, Sinan-gun, 14-vii-2021). 4) Adult, lateral view (same data). 5) A phylogenetic tree for all black weevil COI genes. 6) Distribution map of black weevil in South Korea.
Novel production pathways for the 64Cu / 67Cu theranostic pair through natZn(n, x) reactions
<p>This repository contains all raw gamma-ray spectra analyzed for the present manuscript, as well as calibration spectra. Further details and analysis code are available on reasonable request. </p> <p> </p> <p>The nuclear decay properties of the 64,67Cu radionuclides are favorable for clinical applications, with 64Cu currently being employed for PET imaging. The combined use of 64Cu with 67Cu as a theranostic pair may enable highly personalized therapeutic treatment, with real-time monitoring of dose delivery. In this study, the natZn(n,x) reactions have been investigated as novel production pathways for the 64,67Cu isotopes. The experiment was performed at the Lawrence Berkeley National Laboratory’s 88-Inch Cyclotron, producing fast neutrons through the deuteron breakup process using deuteron beams of 16 MeV and 33 MeV. This study reports spectrum-averaged cross sections for the 64,67Cu isotopes, as well as for 20 additional reaction products from neutron irradiation of natural zinc, zirconium, indium, yttrium and aluminum, more than half of which are measured for the first time. The well-characterized monitor reactions of 89Y(n,2n)88Y, 27Al(n,x)24Na, and natZr(n,x)89Zr were employed to determine the neutron fluence, using the recommendations from the IRDFF-II dosimetry library, and all activities were measured through γ-ray spectroscopy using a high-purity germanium detector. The results are compared to previous experiments from the EXFOR and TENDL-2019 databases, and calculations using ALICE-2017, CoH-3.5.3, EMPIRE-3.2.3, and TALYS-1.9. This work shows that natZn(n,x)64,67Cu is a viable pathway for producing these isotopes, and offers a potential ”tunable” ratio of 64Cu:67Cu for various applications.</p>
Model output data and code for Zhang et al., Cross-cutting scenarios and strategies for designing decarbonization pathways in the transport sector toward carbon neutrality
<p>Model output data and code for "Zhang et al., Cross-cutting scenarios and strategies for designing decarbonization pathways in the transport sector toward carbon neutrality" in Nature Communications.</p>
Galaxy Training Data for "Evaluating and ranking a set of pathways based on multiple metrics"
<pre>This dataset provides the inputs needed for the Galaxy Pathway Analysis workflow training tutorial (<a href="https://galaxy-synbiocad.org">https://galaxy-synbiocad.org</a>). This workflow asseses the performance of predicted pathways by computing 4 criteria (target product flux, thermodynamic feasibility, pathway length, and enzyme availability). A score inform the user about the best candidate pathways to produce a compound of interest. The generated output is a collection of scored and ranked heterologous pathways. The content of the dataset is as follows: - A set of pathways provided in the SBML format (Systems Biology Markup Language) to be ranked, modeling heterologous pathways such as those outputted by the RetroSynthesis workflow (<a href="https://galaxy-synbiocad.org">https://galaxy-synbiocad.org</a>). - The GEM (Genome-scale metabolic models) which is a formalized representation of the metabolism of the host organism (the model is E. coli iML1515), provided in the SBML format.</pre>
Supporting Data for "Decarbonization pathways for the residential sector in the United States"
<p>This repository contains input and processed data for the analysis presented in "Decarbonization pathways for the residential sector in the United States" by Berrill et al. (2022), in Nature Climate Change. </p> <p>Description of the files can be found in the 'Data_Descriptors.docx' file.</p> <p>Please direct any enquiries relating to this dataset to peter.berrill@aya.yale.edu</p>
Dataset for Starting at the community: Treatment seeking pathways of children with suspected severe malaria in Uganda
<p>Dataset for the publication <strong>"Starting at the community: Treatment seeking pathways of children with suspected severe malaria in Uganda".</strong></p> <p>Data from the Community Access to Rectal Artesunate for Malaria (CARAMAL) Project, 2018-2021</p> <p>Descriptive analysis of treatment-seeking pathways of and antimalarial treatment provision for children under 5 years with suspected severe malaria in three districts of Northern Uganda. All children first sought treatment from a community health worker before being referred to a higher-level facility.</p>
Estimating drivers and pathways for hydroelectric reservoir methane emissions using a new mechanistic model (estimated methane emissions for hydropower reservoir surfaces and potential dam emissions)
<p>Methane emissions data from hydropower reservoir surfaces and dams, as estimated with the ResME model. Emissions estimates available for hydropower reservoirs in the GRanD database (Lehner et al., 2011). </p> <p> </p> <p>References:</p> <p>Lehner, B., Liermann, C. Reidy, Revenga, C., Vörösmarty, C., Fekete, B., Crouzet, P., Döll, P., Endejan, M., Frenken, K., Magome, J., Nilsson, C., Robertson, J.C., Rodel, R., Sindorf, N., and Wisser, D. (2011). High-resolution mapping of the world’s reservoirs and dams for sustainable river-flow management. Frontiers in Ecology and the Environment, 9 (9): 494-502. https://doi.org/10.1890/100125.</p>
Data from: Pathways of introduction of alien species in Norway
<p>1. Alien species constitute one of the major threats to global biodiversity. Stopping alien species at an early stage, preferably before establishment, is crucial for the effectiveness of management actions. To enable early detection and prevent future introductions, knowledge of pathways of introduction and their absolute and relative importance is crucial.</p> <p>2. Based on an exhaustive impact assessment of all alien species in Norway (multicellular neobiota), the relation of taxonomy, lifestyle and ecological impact of alien species to their pathways of introduction are investigated. This taxonomically and ecologically unbiased dataset contains 2,267 unique pathways of 1,180 alien species.</p> <p>3. Ecological and taxonomic patterns indicate that terrestrial organisms were predominantly introduced by means of escape (mainly plants escaped from gardens), parasites as contaminants (mainly fungi and insects parasitising plants), freshwater organisms by release (mainly vertebrates), and marine organisms as stowaways (mainly invertebrates and algae). Unaided introductions were most common among insects and marine organisms.</p> <p>4. Alien species with high ecological impact were mainly introduced along the same pathways as other alien species. In relative terms, high-impact species were overrepresented among released species, even though this pathway was subordinate in absolute terms. The number of pathways and the overall introduction pressure were important predictors of ecological impact, especially of the species' invasion potential and area of occupancy.</p> <p>5. Introduction rates of novel alien species have seen recent increases in all taxa and along almost all pathways. This acceleration was especially pronounced for insects and fungi introduced as contaminants and for marine organisms introduced as stowaways. In absolute terms, introduction rates were highest for plant escapes, reaching more than five novel species per year.</p> <p>6. Synthesis and applications: Introduction of new alien species cannot be prevented by closing one or two introduction pathways, since none can be singled out as the main pathway of invasives. Yet each pathway closed makes a difference, as this reduces the overall introduction pressure. The highest priorities for management are the pathways that are easiest to address, such as release, and those with the highest volume, such as plant trade.</p>
Data from: Habitat quality influences pollinator pathogen prevalence through both habitat–disease and biodiversity–disease pathways
<p>The dilution effect hypothesis posits that increasing biodiversity reduces infectious disease transmission. Here, we propose that habitat quality might modulate this negative biodiversity–disease relationship. Habitat may influence pathogen prevalence directly by affecting host traits like nutrition and immune response (we coined this as the 'habitat–disease relationship') or indirectly by changing host biodiversity (biodiversity–disease relationship). We used a path model to test the relative strength of links between habitat, biodiversity, and pathogen prevalence in a pollinator–virus system. High-quality habitat metrics were directly associated with viral prevalence, providing evidence for a habitat–disease relationship. However, the strength and direction of specific habitat effects on viral prevalence varied based on the characteristics of the habitat, host, and pathogen. In general, more natural area and richness of landcover types were directly associated with increased viral prevalence, while greater floral density was associated with reduced viral prevalence. More natural habitat was also indirectly associated with reduced prevalence of two key viruses (black queen cell virus and deformed wing virus) via increased pollinator species richness, providing evidence for a habitat-mediated dilution effect on viral prevalence. Biodiversity–disease relationships varied across viruses, as prevalence of sacbrood virus was not associated with any habitat quality or pollinator community metrics. Across all viruses and hosts, habitat–disease and biodiversity–disease paths had effects of similar magnitude on viral prevalence. Therefore, habitat quality is a key driver of variation in pathogen prevalence among communities via both direct habitat–disease and indirect biodiversity–disease pathways, though the specific patterns varied among different viruses and host species. Critically, habitat–disease relationships could either contribute to or obscure dilution effects in natural systems depending on the relative strength and direction of the habitat–disease and biodiversity–disease pathways in that host–pathogen system. Therefore, habitat may be an important driver in the complex interactions between hosts and pathogens.</p>
Figure 2 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 2 Comparisons and annotations of the official gene set (OGS) of Archegozetes longisetosus.a – Number of gene models of the mites compared to other mites, chelicerates and the fruit fly (Grbić et al., 2011; Cao et al., 2013; dos Santos et al., 2015; Gulia-Nuss et al., 2016; Schwager et al., 2017). b – Non-linear multidimensional scaling plot (NMDS) of clustered orthogroups based on the OGS or predicted proteins
Figure 3 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 3 Orthology comparison and phylogenetic placement of Archegozetes longisetosusamong other chelicerates. a – Maximum likelihood phylogeny based on concatenation of 1,121 orthologs showing the mites phylogenetic position within the Oribatida (all nodes have 100%
Figure 7 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 7 Horizontal gene transfer (HGT) and implications for the feeding biology of Archegozetes longisetosus. a – Blob-plot of the long- read genome assembly contigs plotting the read coverage against GC proportion [%]. Contigs are colored according to the taxonomic order
Figure 6 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 6 The sensory systems of Archegozetes longisetosusand phylogenetic analysis of selected photoreceptor and chemosensory genes. a – Scanning electron micrograph (SEM) showing the end of tarsus on Archegozetes′ first leg. Images shows normal setae, but also modified chemosensory setae, namely eupathidia, both paired (p) and single (s), as well as an omega-3 solenidium. SEM picture courtesy of Michael Heethoff. b – Phylogeny and classification of opsin genes across the Metazoa, including those of several Chelicerata. The tree was constructed using a maximum likelihood approach (LG+F+R4 model) and rooted with a jelly fish opsin. Archegozetes sequences are depicted in red, Drosophila in turquoise; branch length unit is substitutions per site. c – Maximum likelihood phylogeny of ionotropic receptors and ionotropic glutamate receptors (LG+F+R6 model) of Archegozetes (Along), Dinothrombium (Dt), Leptothrombidium (Ld), Tetranychus (Tu) and Drosophila (Dmel). IR25a/IR8a and antenna/1 st leg IRs contain genes with known chemosensory function in Drosophila. The tree was rooted to the middle point; Archegozetes sequences are depicted in red, Drosophila in turquoise; branch length unit is substitutions per site. Bootstrap values can be found in the supplementary Figure S13. d – Maximum likelihood phylogenetic tree of gustatory receptors (JTT+F+R6 model) of Archegozetes(Along), Ixodes (Is), Tropilaelaps (Tm), Metaseiulus (Mocc) and Drosophila (Dmel). The tree was rooted to the middle point; Archegozetessequences are depicted in red, Drosophila in turquoise; branch length unit is substitutions per site. Bootstrap values can be found in the supplementary Figure S14. e – Combined image of volume rendering (grey) and reconstructed nervous system of Archegozetesin dorsal view. Color-code corresponds to different parts of the nervous system, as depicted in the legend. The blue structure in the middle of the synganglion is the part of the esophagus which penetrates the synganglion. Scale bar: 200 µm. Image courtesy of Sebastian Schmelzle based
Figure 1 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 1 The mite, Archegozetes longisetosus, in its phylogenetic and natural environment. a – Species tree of selected oribatid mites of the family Trhypochthoniidae based on phylogenetic analyses and divergence time estimates (Heethoff et al., 2011b). b – Two adults and one tritonymph of Archegozeteson a piece of leaf litter. The algae growing on the leaf serves as a food source for the mites. c – Habitus of an adult mite based on a surface rendering of a µCT-scan reconstruction. Image courtesy of Sebastian Schmelzle. d – Hi-C interaction matrix maps of the nine Archegozeteschromosomes. The corrected contacts are indicated by the color scale on the right from red (high density) to blue (low density)
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.