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331 results for “amoebae”
Input files for simulation of potassium channels using the AMOEBA polarizable force field
<p>This dataset contains input Tinker xyz and key files for the simulation of KcsA potassium channels in DOPC bilayer, a simple script for converting CHARMM pdb file to Tinker xyz file, and modified Tinker source code to support one-dimensional position restraints.<br> "params.tar.gz" contains a description of the force field modifications.<br> <br> To use "mod2", add the following lines to the key file.</p> <pre><code>#compatible with amoebabio18.prm polarize 5 1.4500 0.3900 3 polarize 11 1.4500 0.3900 9 polarize 3 1.7500 0.3900 1 5 7 50 225 227 polarize 9 1.7500 0.3900 1 7 11 50 225 227</code></pre> <p> </p>
Supplementary data for Willemsen et al., 2024 "Novel high-quality amoeba genomes reveal widespread codon usage mismatch between giant viruses and their hosts".
<p>Supplementary data for Willemsen et al., 2024 "Novel high-quality amoeba genomes reveal widespread codon usage mismatch between giant viruses and their hosts". The data set consists of five folders: “Codon_usage_amoebae_and_viruses”, "Genome_annotations_amoebae", "Phylogenetic_trees_18S_amoebae", “Phylogenomic_trees_amoebae”, and "Viral_integration_detection_amoebae". The “Codon_usage_amoebae_and_viruses” folder contains for each amoeba host the calculated codon usage tables in the subfolder "codon_usage_table_host", the calculated codon usage preferences using different scores in the subfolder "codon_usage_scores_host", and the calculated codon usage preferences of giant viruses versus each host in the subfolder "codon_usage_scores_viruses_vs_host". The giant viruses in the subfolder "codon_usage_scores_viruses_vs_host" are organised by viral family and genus in separate sub-subfolders. The "Genome_annotations_amoebae" folder contains the generated genome annotations in different formats and the manually curated mitochondrial genome annotations for each amoeba host. The "Phylogenetic_trees_18S_amoebae" contains for the eukaryotic phyla <em>Discosea</em>, <em>Heterolobosea</em>, and <em>Tubulinea, </em>the 18S rRNA nucleotide alignments, distance matrices, and computed phylogenetic trees. The folder "Phylogenomic_trees_amoebae" contains for the eukaryotic clades <em>Amoebozoa</em> and <em>Discoba, </em>the protein alignment matrices and computed phylogenomic trees. The folder "Viral_integration_detection_amoebae" contains the MCP databases used (fasta file, alignment file, HMM profile and DIAMOND BLASTX database) and the MCP sequences detected in this study and the blast results of these. </p>
Supplementary underlying data for "Evaluating parameterization protocols for hydration free energy calculations with the AMOEBA polarizable force field"
<p>This dataset includes additional underlying data for the publication "Evaluating parameterization protocols for hydration free energy calculations with the AMOEBA polarizable force field"</p> <p>Contents:</p> <p>Tukey Honest Significant Difference (HSD) results for solutes 1-47 across all seven parameter sets, as *.txt. These are pairwise comparisons of results between all possible parameter sets. Significant differences are treated as p < 0.05.</p>
Fig. 5 in Effects of urbanization on the diversity of testate amoebae (Protist, Rhizopoda) in a stream of the southwestern Amazon basin (Igarapé São Francisco in Acre state, Brazil)
Fig. 5. Variation in the mean species richness (A) and density (B) of testate amoebae recorded among the different sampling points on the São Francisco stream in Acre state, northern Brazil.
Fig. 4 in Effects of urbanization on the diversity of testate amoebae (Protist, Rhizopoda) in a stream of the southwestern Amazon basin (Igarapé São Francisco in Acre state, Brazil)
Fig. 4. The most abundant species of testate amoeba recorded in the present study: (A) Netzelia corona, (B) Arcella vulgaris, (C) Arcella brasiliensis, (D) Arcella discoide, (E) Centropyxis aculeata. Examples of the species of testate amoeba recorded in the state of Acre for the first time: (F) Difflugia distenda, (G) Difflugia sinuata, (H) Arcella gandalfi.
Fig. 2 in Effects of urbanization on the diversity of testate amoebae (Protist, Rhizopoda) in a stream of the southwestern Amazon basin (Igarapé São Francisco in Acre state, Brazil)
Fig. 2. Phytophysiognomy of sampling points in the São Francisco stream in the state of Acre, Brazil according to the degree of urbanization.
Fig. 1 in Effects of urbanization on the diversity of testate amoebae (Protist, Rhizopoda) in a stream of the southwestern Amazon basin (Igarapé São Francisco in Acre state, Brazil)
Fig. 1. Location of sampling points on the São Francisco stream in the municipalities of Rio Branco and Bujari, in Acre state, northern Brazil.
Fig. 6 in Effects of urbanization on the diversity of testate amoebae (Protist, Rhizopoda) in a stream of the southwestern Amazon basin (Igarapé São Francisco in Acre state, Brazil)
Fig. 6. Biplot of the first two axes of the Redundancy Analysis of the scores of the streams according to the abiotic variables (TC = Thermotolerant Coliforms; EC = Electrical Conductivity, DO = Oxygen; pH = Hydrogen potential; TotP = Total Phosphorus; Temp = Temperature; Turb = Turbidity; NH 4 = Ammonia; NO 2 = Nitrate), the legend explains the symbols corresponding to the family names.
Fig. 7 in Certesella larai (Amoebozoa: Arcellinida: Hyalospheniformes) a new soil testate amoeba species from the Dominican Republic and Chile challenges the definition of genera Certesella and Porosia
Fig. 7. Maximum range of shell length and width of the three known Certesella and Porosia species showing a lack of overlap between C. larai n.sp. and all other species from the two genera in this two-dimensional space. Each species is illustrated (images not exactly to scale).
Fig. 6 in Certesella larai (Amoebozoa: Arcellinida: Hyalospheniformes) a new soil testate amoeba species from the Dominican Republic and Chile challenges the definition of genera Certesella and Porosia
Fig. 6. Comparative overview of the morphology of all known species of genera Certesella and Porosia species. A: Certesella larai n. sp., B: C. certesi, C: C. australis, D: C. murrayi, E: C. martiali, F: Porosia paracarinata, G: P. bigibbbosa. Images are not to scale as some early images lacked a scale.
Fig. 5 in Certesella larai (Amoebozoa: Arcellinida: Hyalospheniformes) a new soil testate amoeba species from the Dominican Republic and Chile challenges the definition of genera Certesella and Porosia
Fig. 5. Biplot of length vs. width of two populations of Certesella larai n.sp. from Dominican Republic and Chile.
Fig. 3 in Certesella larai (Amoebozoa: Arcellinida: Hyalospheniformes) a new soil testate amoeba species from the Dominican Republic and Chile challenges the definition of genera Certesella and Porosia
Fig. 3. Light microscopy images of Certesella larai n.sp. from Parque Nacional Alerce Costero, Los Ríos Region, Chile, showing the detail of the pseudostome. The right image shows internal teeth fully visible on the flank of the neck (solid arrow and visible only in transparency (empty arrow). Such structures are only visible in ca. 10% of the specimens. Scale bar 10 µm.
Fig. 1 in Certesella larai (Amoebozoa: Arcellinida: Hyalospheniformes) a new soil testate amoeba species from the Dominican Republic and Chile challenges the definition of genera Certesella and Porosia
Fig. 1. General shape of Certesella larai n.sp. and indication of the morphometrical measurements. 1 – shell length, 2 – shell breadth, 3 – shell length / breadth ratio (not illustrated), 4 – aperture (long axis), 5 – distance from fundus to the pores, 6 – distance from fundus to base of neck, 7 – distance between the pores, 8 – width of the neck at narrowest point, 9 – pore length, 10 – pore width.
Fig. 2 in Certesella larai (Amoebozoa: Arcellinida: Hyalospheniformes) a new soil testate amoeba species from the Dominican Republic and Chile challenges the definition of genera Certesella and Porosia
Fig. 2. Light microscopy images of Certesella larai n.sp. from Parque Nacional Alerce Costero, Los Ríos Region, Chile. Left: DIC image of the type specimen deposited at the Natural History Museum of Neuchâtel (slide 95–2). Centre and right: brightfield images of specimens from the same sample. Scale bar 20 µm.
Fig. 3 in Effects of urbanization on the diversity of testate amoebae (Protist, Rhizopoda) in a stream of the southwestern Amazon basin (Igarapé São Francisco in Acre state, Brazil)
Fig. 3. Plot of the results of the Principal Components Analysis (PCA) of the environmental variables of the São Francisco stream in Rio Branco e Bujari, Acre (Brazil): TC = Thermotolerant Coliforms; EC = Electrical Conductivity; pH = Hydrogen potential; DO = Oxygen; TotP = Total Phosphorus; Phos = Phosphate; Temp = Temperature; Transp = Transparency; Turb = Turbidity; FR = Flow Rate; Dep = Depth; NH 4 = Ammonia; NO 3 = Nitrite; NO 2 = Nitrate.
Fig. 3 in Testate Amoeba Communities of Epilithic Mosses and Lichens: New Data from Russia, Switzerland and Italy
Fig. 3. Taxon richness (A) and test concentration (B) against moisture content expressed as a proportion.
Fig. 6 in Exploring the diversity and ecology of testate amoebae in West Siberian peatlands
Fig. 6. Plots of taxon abundance versus moisture content for the twelve most abundant testate amoeba taxa. All taxa show a significant correlation with moisture (Spearman Rs, P <0.05) with the exception of Nebela tincta.
Fig. 2 in Exploring the diversity and ecology of testate amoebae in West Siberian peatlands
Fig. 2. Author location based on institutional details for 652 publications listed in SCOPUS containing the phrase 'testate amoebae' in keywords, abstract and title. SCOPUS is not a comprehensive source of data on testate amoeba publication (probable biases towards the more recent and English language literature) but provides a reasonable representation of the overall state of the literature. Colour density is proportional to number of publications with grey shading for countries with no identified publications. Map created using the StatSilk mapper tool.
Fig. 1 in Exploring the diversity and ecology of testate amoebae in West Siberian peatlands
Fig. 1. Trends in publications including the phrase 'testate amoebae' in title, keywords or abstract as determined by a SCOPUS search February 2017. Database publication trends are not necessarily an accurate reflection of quantity of research as not all older material is digitized and there has been a general trend for researchers to publish a greater number of shorter papers. However results are comparable between search terms so it is interesting to note the same data for 'naked amoebae' as a comparison. An important driver of increasing research is palaeoecology and some key events are highlighted for comparison.
Fig. 2 in Testate Amoeba Communities of Epilithic Mosses and Lichens: New Data from Russia, Switzerland and Italy
Fig. 2. Taxon richness (A), Simpson diversity (B) and test concentration (C) by region. Bars show mean and error bars the standard deviation. Letters denote significant differences (P <0.05) where the global test is significant, see text for details.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.