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Monitoring permafrost thaw in Denali National Park and Preserve: year one of data collection 2013
Transects were established at six sites in the Toklat river basin, Denali National Park and Preserve. This was the fist year of what will be a long-term monitoring project of permafrost and ecosystem characteristics. Transects were co-located with known thaw subsidence (thermokarst) features and run from outside (relatively undisturbed tundra) through the feature.
Figure 5 in Does your preservative preserve? A comparison of the efficacy of some pitfall trap solutions in preserving the internal reproductive organs of dung beetles
Figure 5. Pitfall trap with protective caging and cover placed on-top of a manually constructed soil mound so as to prevent interference from mammals and dilution and/or overspilling from precipitation and surface runoff.
Figure 2. L in Does your preservative preserve? A comparison of the efficacy of some pitfall trap solutions in preserving the internal reproductive organs of dung beetles
Figure 2. L. militaris (female) after 28 days of submergence in 4% PBF showing the well preserved ovary and oocytes.
Figure 3 in Does your preservative preserve? A comparison of the efficacy of some pitfall trap solutions in preserving the internal reproductive organs of dung beetles
Figure 3. Evaporation rates of the eight preservatives in the riparian vine thicket environment. Water is also shown for comparison. The dotted line represents the critical volume. PG = propylene glycol, w vinegar = white vinegar.
Figure 4 in Does your preservative preserve? A comparison of the efficacy of some pitfall trap solutions in preserving the internal reproductive organs of dung beetles
Figure 4. Evaporation rates of the eight preservatives in the low open woodland environment. Water is also shown for comparison. The dotted line represents the critical volume. PG = propylene glycol, w vinegar = white vinegar.
Fig. 3. A–C in Description of a new species of Paracrobeles Heyns, 1968 (Nematoda, Rhabditida, Cephalobidae) from Kelso Dunes, Mojave National Preserve, California, USA
Fig. 3. A–C. Paracrobeles kelsodunensis sp. nov. LM micrographs. A. Male anterior end, ventral side to the right. B–C. Female anterior end, ventral side to the right. D–H. Paracrobeles mojavicus Taylor, Baldwin & Mundo-Ocampo, 2004. D–F. Female anterior end, ventral side to the right. G–H. Male anterior end, ventral side to the right. I. Paracrobeles cf. kelsodunensis sp. nov., male anterior end, ventral side to the right. Scale bar: A–I = 10 µm.
Fig. 1 in Description of a new species of Paracrobeles Heyns, 1968 (Nematoda, Rhabditida, Cephalobidae) from Kelso Dunes, Mojave National Preserve, California, USA
Fig. 1. Paracrobeles kelsodunensis sp. nov. A. Pharyngeal region. B. Female gonad. C. Female tail. D. Male tail. Scale bar = 20 µm.
In-place molecular preservation of cellulose in 5000-year-old archaeological textiles
<p>AFM-IR, FT-IR, SHG and µCT datasets associated to the paper "In-place molecular preservation of cellulose in 5000-year-old archaeological textiles"</p>
Figures 11-21 in Neotropical Pentatomidae (Insecta: Hemiptera: Heteroptera) of the collection of Massimiliano Spinola preserved in the "Museo Regionale de Scienze Naturali"̡ Turin̡ Italy
Figures 11-21. Types of Neotropical Pentatomidae of the Spinola Collection̡ Museo Regionale de Scienze Naturali̡ Turin. Genitalia: (11-12) Arvelius gladiator̡ male lectotype: (11) posterior view; (12) ventral view; (13-14) Cataulax macraspis̡ male holotype: (13) posterior view; (14) ventral view; (15-16) Schaefferella litigiosa̡ male lectotype: (15) posterior view; (16) ventral view; (17) Chlorocoris tau̡ female lectotype̡ ventral view; (18) Audinetella bipunctata̡ female lectotype̡ posteroventral view; (19) Ochlerus cinctus̡ female lectotype̡ posteroventral view; (20) Vulsirea ancora̡ female holotype̡ ventral view; (21) Vulsirea nigrorubra̡ female holotype̡ ventral view. Scales = 1 mm.
Figures 3-10 in Neotropical Pentatomidae (Insecta: Hemiptera: Heteroptera) of the collection of Massimiliano Spinola preserved in the "Museo Regionale de Scienze Naturali"̡ Turin̡ Italy
Figures 3-10. Types of Neotropical Pentatomidae of the Spinola Collection̡ Museo Regionale de Scienze Naturali̡ Turin. Dorsal facies: (3) Chlorocoris tau̡ female lectotype; (4) Arvelius gladiator̡ male lectotype; (5) Audinetella bipunctata̡ female lectotype; (6) Cataulax macraspis̡ male holotype; (7) Schaefferella litigiosa̡ male lectotype; (8) Ochlerus cinctus̡ female lectotype; (9) Vulsirea ancora̡ female holotype; (10) Vulsirea nigrorubra̡ female holotype. Scales = 2 mm.
FIG. 5 in Anatomical preservation of silicified Corylites J.S.Gardner leaves from the Paleocene maar lake of Menat (Puy-de-Dôme, France)
FIG. 5. — SEM images of anatomical details of the silicified leaf of Corylites macquarrii (Forbes) Heer shown in Fig. 2A from the Paleocene of Menat (Inv.-No. MMM-2010-019): A, overview of an area with parenchymatic cells and tracheids (top right); B, close-up of tracheids; to the left, a tracheid with a silicified scalariform pitted cell wall, to the right the honeycomb-like infilling of a tracheid; C, detail of the tracheid with scalariform pitting, exhibiting silicified fungal hyphae or ascomycete filaments; D, overview of an area with a minor tracheid; E, detail of a minor tracheid where only former spiral thickenings of the cell walls have been silicified; F, detail of a minor tracheid where only small areas of the thin cell wall areas have been silicified between spiral thickenings of the cell walls. Scale bars: A, 10 µm; B, F, 5 µm; C, E, 2 µm; D, 20 µm.
FIG. 3 in Anatomical preservation of silicified Corylites J.S.Gardner leaves from the Paleocene maar lake of Menat (Puy-de-Dôme, France)
FIG. 3. — Results of a qualitative EDX analysis of a silicified leaf of Corylites macquarrii (FORBES) HEER from Menat (Inv.-No. MMM-2010-019): A, SEM image of the same area of the silicified leaf analyzed by EDX; B, qualitative EDX spectrum of the area shown in A, exhibiting strong Si and O peaks, together with minor C and Al peaks. Spectrum is cut off at 5 kV, as no further peaks appeared beyond this value.
FIG. 2 in Anatomical preservation of silicified Corylites J.S.Gardner leaves from the Paleocene maar lake of Menat (Puy-de-Dôme, France)
FIG. 2. — Examples of silicified leaves from the Paleocene of Menat: A, Corylites macquarrii (Forbes) Heer, Inv.-No. MMM-2010-019; B, cf. Corylites macquarrii (Forbes) Heer, Inv.-No. MMM-2010-012. Scale bars: 2 cm.
FIG. 1 in Anatomical preservation of silicified Corylites J.S.Gardner leaves from the Paleocene maar lake of Menat (Puy-de-Dôme, France)
FIG. 1. — Map of France showing the geographic position of Menat. (Source: http://d-maps.com/m/europa/france/france/france09.gif).
Data from: Preserved collagen reveals species identity in archaeological marine turtle bones from Caribbean and Florida sites
Advancements in molecular science are continually improving our understanding of marine turtle biology and evolution. However, there are still considerable gaps in our understanding, such as past marine turtle distributions, which can benefit from advanced zooarchaeological analyses. Here we apply collagen fingerprinting to 130 archaeological marine turtle bone samples up to 2500 years old from the Caribbean and Florida's Gulf Coast for faunal identification, finding the vast majority of samples (88%) to contain preserved collagen despite deposition in the tropics. All samples can be identified to species-level with the exception of the Kemp's ridley (Lepidochelys kempii) and olive ridley (L. olivacea) turtles, which can be separated to genus level, having diverged from one another only ~5 million years ago. Additionally, we identify a single homologous peptide that allows the separation of archaeological green turtle samples, Chelonia spp., into two distinct groups, which potentially signifies a difference in genetic stock. The majority of the archaeological samples are identified as green turtle (Chelonia spp.; 63%), with hawksbill (Eretmochelys imbricata; 17%) and ridley turtles (Lepidochelys spp.; 3%) making up smaller proportions of the assemblage. There were no molecular identifications of the loggerhead turtle (Caretta caretta) in the assemblage despite 9% of the samples being morphologically identified as such, highlighting the difficulties in relying on morphological identifications alone in archaeological remains. Finally, we present the first marine turtle molecular phylogeny using collagen (I) amino acid sequences and find our analyses match recent phylogenies based on nuclear and mitochondrial DNA. Our results highlight the advantage of using collagen fingerprinting to supplement morphological analyses of turtle bones and support the usefulness of this technique for assessing their past distributions across the Caribbean and Florida's Gulf Coast, especially in these tropical environments where DNA preservation may be poor.
Heatmaps of orthology and protein domain preservation in RNA Processing complexes throughout the fungal kingdom
<p>An analysis of the presence/absence of orthologues for Fungal RNA Processing protein complexes, and the presence/absence of the known PFAM protein domains within each protein within these complexes in the organism's proteome. </p> <p>Each image represents one RNA Processing protein complex.</p> <p>Orthology (far left panel in each image) is relative to Yeast, and taken from a query against the EnsEMBL orthology database (black = no orthologue; red = orthologue). <br> <br> Each orthologue was then queried for its PFAM domains, and the non-redundant set of PFAM domains representing each set of orthologous proteins, spanning all species, was then scanned against the complete proteome of each species. The resulting heatmap indicates the presence or absence of that PFAM domain anywhere in the proteome of that species. (black = absent; red = 1 copy; grey->blue = more than one copy)</p>
CERN Analysis Preservation User Stories
<p>This comic-like drawing is a graphical representation of the User Stories identified for CERN Analysis Preservation.</p>
Autopolyploidy Genome Duplication Preserves Other Ancient Genome Duplications in Atlantic Salmon (Salmo salar) Supplementary Datasets
<p>For various species, alignments were found between a protein database (produced from Zebrafish) and the sequenced genome of that species. Using Perl scripts and the alignments, gene models were identified in the various species based on the protein sequences. </p> <ul> <li>The gene models, for the various species, can be found in the .gff3 files. Some of the .gff3 files have had ribosomal proteins removed. </li> <li>Homeologous regions were then identified using Perl scripts and can be found in .gff3 files as well. They have Homeologous_Regions.gff3 in their title. </li> <li>Homeologous genes in these regions were counted (named XX_XX_Homeologous_Regions.txt), and compared to all of the genes (not just homeologous genes) in these regions (named Gene_Count_Homeolgous_XX_XX_XX.txt) to find the density. </li> <li>Homeologous gene sequences were compared to each other to identify the Ps values between them using a program called SNAP (Files with _Homeologous_region_analysis_version_1.2.txt at the end). </li> <li>The analyses of these files are summarized in "Pn_Ps_Values_Vertebrate_Homeologous_Regions.ods." </li> <li>The synteny between species can be found in the files with .seg extensions (These can be opened in IGV). </li> <li>A comparison between the gene density and Ps value for each homeologous region can be found in the file, "Gene_Density_Compared_to_Ps_Values.ods."</li> </ul> <p>Included is an extended readme file and Perl scripts (.pl extension) in a compressed file (Final_Scripts.tar.gz).</p>
A geometry preserving, conservative, mesh-to-mesh isogeometric interpolation algorithm for spatial adaptivity of the multigroup, second-order even-parity form of the neutron transport equation
<p>In this paper a method is presented for the application of energy-dependent spatial meshes applied to the multigroup, second-order, even-parity form of the neutron transport equation using Isogeometric Analysis (IGA). The computation of the inter-group regenerative source terms is based on conservative interpolation by Galerkin projection. The use of Non-Uniform Rational B-splines (NURBS) from the original computer-aided design (CAD) model allows for efficient implementation and calculation of the spatial projection operations while avoiding the complications of matching different geometric approximations faced by traditional finite element methods (FEM). The rate-of-convergence was verified using the method of manufactured solutions (MMS) and found to preserve the theoretical rates when interpolating between spatial meshes of different refinements. The scheme’s numerical efficiency was then studied using a series of two-energy group pincell test cases where a significant saving in the number of degrees-of-freedom can be found if the energy group with a complex variation in the solution is refined more than an energy group with a simpler solution function. Finally, the method was applied to a heterogeneous, seven-group reactor pincell where the spatial meshes for each energy group were adaptively selected for refinement. It was observed that by refining selected energy groups a reduction in the total number of degrees-of-freedom for the same total L2 error can be obtained.</p>
FIG. 2. — Holotype MNHN.F.B16583 in A new species of mecochirid lobster from the Late Cretaceous of France, preserved with its eggs
FIG. 2. — Holotype MNHN.F.B16583 (Triger coll.) of Mecochirus cenomanicus n. sp. from the Cenomanian of La Butte quarry, Le Mans, France: part and counterpart (A, C) and interpretative live drawing (B); white frame corresponds to SEM images and EDS analysis. Abbreviations: a, branchiocardiac groove; a2, antenna; b, antennal groove; ba, basipodite; b1, hepatic groove; c, postcervical groove; cd, cardiac groove; d, gastro-orbital groove; di, diaeresis; e, eye; en, uropodal endopod; ex, uropodal exopod; e1e, cervical groove; gc, gastro-orbital carina; oc, orbital carina; P1-P5, pereiopods 1 to 5; r, rostrum; sc, scaphocerite; s1–s6, pleonal somites 1 to 6; t, telson. Photographs: P. Loubry. Line drawing: R. Gilardet. Scale bars: 5 mm.
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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.